LUYAO REN
před 4 roky
1 změnil soubory, kde provedl 30 přidání a 10 odebrání
+ 30
- 10
tasks/bedAnnotation.wdl
Zobrazit soubor
| @@ -11,37 +11,57 @@ task bedAnnotation { | |||
| # filtered | |||
| # BND | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1450.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1350.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1250.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1150.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1050.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.950.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.850.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.750.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.650.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.550.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.450.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.350.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.250.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.150.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.50.left.bed ${breakpoint_directory}/D5.BND.50.right.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.150.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.250.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.350.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.450.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.550.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.650.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.750.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.850.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.950.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1050.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1150.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1250.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1350.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1450.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed > ${sample_name}.BND.filtered.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1450.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1350.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1250.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1150.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1050.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.950.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.850.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.750.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.650.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.550.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.450.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.350.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.250.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.150.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.50.left.bed ${breakpoint_directory}/D5.BND.50.right.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.150.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.250.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.350.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.450.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.550.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.650.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.750.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.850.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.950.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1050.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1150.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1250.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1350.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1450.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed > ${sample_name}.BND.filtered.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.BND.4900.left.bed ${breakpoint_directory}/D5.BND.4800.left.bed ${breakpoint_directory}/D5.BND.4700.left.bed ${breakpoint_directory}/D5.BND.4600.left.bed ${breakpoint_directory}/D5.BND.4500.left.bed ${breakpoint_directory}/D5.BND.4400.left.bed ${breakpoint_directory}/D5.BND.4300.left.bed ${breakpoint_directory}/D5.BND.4200.left.bed ${breakpoint_directory}/D5.BND.4100.left.bed ${breakpoint_directory}/D5.BND.4000.left.bed ${breakpoint_directory}/D5.BND.3900.left.bed ${breakpoint_directory}/D5.BND.3800.left.bed ${breakpoint_directory}/D5.BND.3700.left.bed ${breakpoint_directory}/D5.BND.3600.left.bed ${breakpoint_directory}/D5.BND.3500.left.bed ${breakpoint_directory}/D5.BND.3400.left.bed ${breakpoint_directory}/D5.BND.3300.left.bed ${breakpoint_directory}/D5.BND.3200.left.bed ${breakpoint_directory}/D5.BND.3100.left.bed ${breakpoint_directory}/D5.BND.3000.left.bed ${breakpoint_directory}/D5.BND.2900.left.bed ${breakpoint_directory}/D5.BND.2800.left.bed ${breakpoint_directory}/D5.BND.2700.left.bed ${breakpoint_directory}/D5.BND.2600.left.bed ${breakpoint_directory}/D5.BND.2500.left.bed ${breakpoint_directory}/D5.BND.2400.left.bed ${breakpoint_directory}/D5.BND.2300.left.bed ${breakpoint_directory}/D5.BND.2200.left.bed ${breakpoint_directory}/D5.BND.2100.left.bed ${breakpoint_directory}/D5.BND.2000.left.bed ${breakpoint_directory}/D5.BND.1900.left.bed ${breakpoint_directory}/D5.BND.1800.left.bed ${breakpoint_directory}/D5.BND.1700.left.bed ${breakpoint_directory}/D5.BND.1600.left.bed ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed ${breakpoint_directory}/D5.BND.1600.right.bed ${breakpoint_directory}/D5.BND.1700.right.bed ${breakpoint_directory}/D5.BND.1800.right.bed ${breakpoint_directory}/D5.BND.1900.right.bed ${breakpoint_directory}/D5.BND.2000.right.bed ${breakpoint_directory}/D5.BND.2100.right.bed ${breakpoint_directory}/D5.BND.2200.right.bed ${breakpoint_directory}/D5.BND.2300.right.bed ${breakpoint_directory}/D5.BND.2400.right.bed ${breakpoint_directory}/D5.BND.2500.right.bed ${breakpoint_directory}/D5.BND.2600.right.bed ${breakpoint_directory}/D5.BND.2700.right.bed ${breakpoint_directory}/D5.BND.2800.right.bed ${breakpoint_directory}/D5.BND.2900.right.bed ${breakpoint_directory}/D5.BND.3000.right.bed ${breakpoint_directory}/D5.BND.3100.right.bed ${breakpoint_directory}/D5.BND.3200.right.bed ${breakpoint_directory}/D5.BND.3300.right.bed ${breakpoint_directory}/D5.BND.3400.right.bed ${breakpoint_directory}/D5.BND.3500.right.bed ${breakpoint_directory}/D5.BND.3600.right.bed ${breakpoint_directory}/D5.BND.3700.right.bed ${breakpoint_directory}/D5.BND.3800.right.bed ${breakpoint_directory}/D5.BND.3900.right.bed ${breakpoint_directory}/D5.BND.4000.right.bed ${breakpoint_directory}/D5.BND.4100.right.bed ${breakpoint_directory}/D5.BND.4200.right.bed ${breakpoint_directory}/D5.BND.4300.right.bed ${breakpoint_directory}/D5.BND.4400.right.bed ${breakpoint_directory}/D5.BND.4500.right.bed ${breakpoint_directory}/D5.BND.4600.right.bed ${breakpoint_directory}/D5.BND.4700.right.bed ${breakpoint_directory}/D5.BND.4800.right.bed ${breakpoint_directory}/D5.BND.4900.right.bed > ${sample_name}.BND.filtered.txt | |||
| # DEL | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1450.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1350.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1250.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1150.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1050.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.950.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.850.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.750.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.650.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.550.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.450.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.350.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.250.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.150.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.50.left.bed ${breakpoint_directory}/D5.DEL.50.right.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.150.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.250.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.350.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.450.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.550.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.650.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.750.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.850.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.950.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1050.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1150.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1250.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1350.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1450.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed > ${sample_name}.DEL.filtered.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1450.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1350.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1250.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1150.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1050.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.950.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.850.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.750.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.650.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.550.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.450.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.350.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.250.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.150.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.50.left.bed ${breakpoint_directory}/D5.DEL.50.right.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.150.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.250.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.350.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.450.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.550.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.650.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.750.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.850.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.950.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1050.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1150.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1250.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1350.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1450.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed > ${sample_name}.DEL.filtered.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DEL.4900.left.bed ${breakpoint_directory}/D5.DEL.4800.left.bed ${breakpoint_directory}/D5.DEL.4700.left.bed ${breakpoint_directory}/D5.DEL.4600.left.bed ${breakpoint_directory}/D5.DEL.4500.left.bed ${breakpoint_directory}/D5.DEL.4400.left.bed ${breakpoint_directory}/D5.DEL.4300.left.bed ${breakpoint_directory}/D5.DEL.4200.left.bed ${breakpoint_directory}/D5.DEL.4100.left.bed ${breakpoint_directory}/D5.DEL.4000.left.bed ${breakpoint_directory}/D5.DEL.3900.left.bed ${breakpoint_directory}/D5.DEL.3800.left.bed ${breakpoint_directory}/D5.DEL.3700.left.bed ${breakpoint_directory}/D5.DEL.3600.left.bed ${breakpoint_directory}/D5.DEL.3500.left.bed ${breakpoint_directory}/D5.DEL.3400.left.bed ${breakpoint_directory}/D5.DEL.3300.left.bed ${breakpoint_directory}/D5.DEL.3200.left.bed ${breakpoint_directory}/D5.DEL.3100.left.bed ${breakpoint_directory}/D5.DEL.3000.left.bed ${breakpoint_directory}/D5.DEL.2900.left.bed ${breakpoint_directory}/D5.DEL.2800.left.bed ${breakpoint_directory}/D5.DEL.2700.left.bed ${breakpoint_directory}/D5.DEL.2600.left.bed ${breakpoint_directory}/D5.DEL.2500.left.bed ${breakpoint_directory}/D5.DEL.2400.left.bed ${breakpoint_directory}/D5.DEL.2300.left.bed ${breakpoint_directory}/D5.DEL.2200.left.bed ${breakpoint_directory}/D5.DEL.2100.left.bed ${breakpoint_directory}/D5.DEL.2000.left.bed ${breakpoint_directory}/D5.DEL.1900.left.bed ${breakpoint_directory}/D5.DEL.1800.left.bed ${breakpoint_directory}/D5.DEL.1700.left.bed ${breakpoint_directory}/D5.DEL.1600.left.bed ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed ${breakpoint_directory}/D5.DEL.1600.right.bed ${breakpoint_directory}/D5.DEL.1700.right.bed ${breakpoint_directory}/D5.DEL.1800.right.bed ${breakpoint_directory}/D5.DEL.1900.right.bed ${breakpoint_directory}/D5.DEL.2000.right.bed ${breakpoint_directory}/D5.DEL.2100.right.bed ${breakpoint_directory}/D5.DEL.2200.right.bed ${breakpoint_directory}/D5.DEL.2300.right.bed ${breakpoint_directory}/D5.DEL.2400.right.bed ${breakpoint_directory}/D5.DEL.2500.right.bed ${breakpoint_directory}/D5.DEL.2600.right.bed ${breakpoint_directory}/D5.DEL.2700.right.bed ${breakpoint_directory}/D5.DEL.2800.right.bed ${breakpoint_directory}/D5.DEL.2900.right.bed ${breakpoint_directory}/D5.DEL.3000.right.bed ${breakpoint_directory}/D5.DEL.3100.right.bed ${breakpoint_directory}/D5.DEL.3200.right.bed ${breakpoint_directory}/D5.DEL.3300.right.bed ${breakpoint_directory}/D5.DEL.3400.right.bed ${breakpoint_directory}/D5.DEL.3500.right.bed ${breakpoint_directory}/D5.DEL.3600.right.bed ${breakpoint_directory}/D5.DEL.3700.right.bed ${breakpoint_directory}/D5.DEL.3800.right.bed ${breakpoint_directory}/D5.DEL.3900.right.bed ${breakpoint_directory}/D5.DEL.4000.right.bed ${breakpoint_directory}/D5.DEL.4100.right.bed ${breakpoint_directory}/D5.DEL.4200.right.bed ${breakpoint_directory}/D5.DEL.4300.right.bed ${breakpoint_directory}/D5.DEL.4400.right.bed ${breakpoint_directory}/D5.DEL.4500.right.bed ${breakpoint_directory}/D5.DEL.4600.right.bed ${breakpoint_directory}/D5.DEL.4700.right.bed ${breakpoint_directory}/D5.DEL.4800.right.bed ${breakpoint_directory}/D5.DEL.4900.right.bed > ${sample_name}.DEL.filtered.txt | |||
| # INS | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1450.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1350.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1250.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1150.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1050.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.950.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.850.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.750.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.650.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.550.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.450.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.350.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.250.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.150.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.50.left.bed ${breakpoint_directory}/D5.INS.50.right.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.150.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.250.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.350.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.450.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.550.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.650.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.750.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.850.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.950.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1050.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1150.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1250.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1350.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1450.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed > ${sample_name}.INS.filtered.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1450.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1350.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1250.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1150.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1050.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.950.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.850.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.750.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.650.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.550.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.450.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.350.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.250.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.150.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.50.left.bed ${breakpoint_directory}/D5.INS.50.right.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.150.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.250.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.350.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.450.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.550.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.650.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.750.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.850.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.950.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1050.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1150.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1250.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1350.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1450.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed > ${sample_name}.INS.filtered.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INS.4900.left.bed ${breakpoint_directory}/D5.INS.4800.left.bed ${breakpoint_directory}/D5.INS.4700.left.bed ${breakpoint_directory}/D5.INS.4600.left.bed ${breakpoint_directory}/D5.INS.4500.left.bed ${breakpoint_directory}/D5.INS.4400.left.bed ${breakpoint_directory}/D5.INS.4300.left.bed ${breakpoint_directory}/D5.INS.4200.left.bed ${breakpoint_directory}/D5.INS.4100.left.bed ${breakpoint_directory}/D5.INS.4000.left.bed ${breakpoint_directory}/D5.INS.3900.left.bed ${breakpoint_directory}/D5.INS.3800.left.bed ${breakpoint_directory}/D5.INS.3700.left.bed ${breakpoint_directory}/D5.INS.3600.left.bed ${breakpoint_directory}/D5.INS.3500.left.bed ${breakpoint_directory}/D5.INS.3400.left.bed ${breakpoint_directory}/D5.INS.3300.left.bed ${breakpoint_directory}/D5.INS.3200.left.bed ${breakpoint_directory}/D5.INS.3100.left.bed ${breakpoint_directory}/D5.INS.3000.left.bed ${breakpoint_directory}/D5.INS.2900.left.bed ${breakpoint_directory}/D5.INS.2800.left.bed ${breakpoint_directory}/D5.INS.2700.left.bed ${breakpoint_directory}/D5.INS.2600.left.bed ${breakpoint_directory}/D5.INS.2500.left.bed ${breakpoint_directory}/D5.INS.2400.left.bed ${breakpoint_directory}/D5.INS.2300.left.bed ${breakpoint_directory}/D5.INS.2200.left.bed ${breakpoint_directory}/D5.INS.2100.left.bed ${breakpoint_directory}/D5.INS.2000.left.bed ${breakpoint_directory}/D5.INS.1900.left.bed ${breakpoint_directory}/D5.INS.1800.left.bed ${breakpoint_directory}/D5.INS.1700.left.bed ${breakpoint_directory}/D5.INS.1600.left.bed ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed ${breakpoint_directory}/D5.INS.1600.right.bed ${breakpoint_directory}/D5.INS.1700.right.bed ${breakpoint_directory}/D5.INS.1800.right.bed ${breakpoint_directory}/D5.INS.1900.right.bed ${breakpoint_directory}/D5.INS.2000.right.bed ${breakpoint_directory}/D5.INS.2100.right.bed ${breakpoint_directory}/D5.INS.2200.right.bed ${breakpoint_directory}/D5.INS.2300.right.bed ${breakpoint_directory}/D5.INS.2400.right.bed ${breakpoint_directory}/D5.INS.2500.right.bed ${breakpoint_directory}/D5.INS.2600.right.bed ${breakpoint_directory}/D5.INS.2700.right.bed ${breakpoint_directory}/D5.INS.2800.right.bed ${breakpoint_directory}/D5.INS.2900.right.bed ${breakpoint_directory}/D5.INS.3000.right.bed ${breakpoint_directory}/D5.INS.3100.right.bed ${breakpoint_directory}/D5.INS.3200.right.bed ${breakpoint_directory}/D5.INS.3300.right.bed ${breakpoint_directory}/D5.INS.3400.right.bed ${breakpoint_directory}/D5.INS.3500.right.bed ${breakpoint_directory}/D5.INS.3600.right.bed ${breakpoint_directory}/D5.INS.3700.right.bed ${breakpoint_directory}/D5.INS.3800.right.bed ${breakpoint_directory}/D5.INS.3900.right.bed ${breakpoint_directory}/D5.INS.4000.right.bed ${breakpoint_directory}/D5.INS.4100.right.bed ${breakpoint_directory}/D5.INS.4200.right.bed ${breakpoint_directory}/D5.INS.4300.right.bed ${breakpoint_directory}/D5.INS.4400.right.bed ${breakpoint_directory}/D5.INS.4500.right.bed ${breakpoint_directory}/D5.INS.4600.right.bed ${breakpoint_directory}/D5.INS.4700.right.bed ${breakpoint_directory}/D5.INS.4800.right.bed ${breakpoint_directory}/D5.INS.4900.right.bed > ${sample_name}.INS.filtered.txt | |||
| # INV | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1450.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1350.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1250.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1150.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1050.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.950.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.850.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.750.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.650.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.550.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.450.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.350.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.250.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.150.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.50.left.bed ${breakpoint_directory}/D5.INV.50.right.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.150.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.250.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.350.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.450.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.550.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.650.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.750.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.850.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.950.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1050.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1150.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1250.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1350.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1450.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed > ${sample_name}.INV.filtered.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1450.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1350.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1250.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1150.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1050.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.950.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.850.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.750.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.650.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.550.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.450.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.350.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.250.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.150.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.50.left.bed ${breakpoint_directory}/D5.INV.50.right.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.150.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.250.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.350.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.450.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.550.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.650.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.750.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.850.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.950.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1050.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1150.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1250.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1350.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1450.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed > ${sample_name}.INV.filtered.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INV.4900.left.bed ${breakpoint_directory}/D5.INV.4800.left.bed ${breakpoint_directory}/D5.INV.4700.left.bed ${breakpoint_directory}/D5.INV.4600.left.bed ${breakpoint_directory}/D5.INV.4500.left.bed ${breakpoint_directory}/D5.INV.4400.left.bed ${breakpoint_directory}/D5.INV.4300.left.bed ${breakpoint_directory}/D5.INV.4200.left.bed ${breakpoint_directory}/D5.INV.4100.left.bed ${breakpoint_directory}/D5.INV.4000.left.bed ${breakpoint_directory}/D5.INV.3900.left.bed ${breakpoint_directory}/D5.INV.3800.left.bed ${breakpoint_directory}/D5.INV.3700.left.bed ${breakpoint_directory}/D5.INV.3600.left.bed ${breakpoint_directory}/D5.INV.3500.left.bed ${breakpoint_directory}/D5.INV.3400.left.bed ${breakpoint_directory}/D5.INV.3300.left.bed ${breakpoint_directory}/D5.INV.3200.left.bed ${breakpoint_directory}/D5.INV.3100.left.bed ${breakpoint_directory}/D5.INV.3000.left.bed ${breakpoint_directory}/D5.INV.2900.left.bed ${breakpoint_directory}/D5.INV.2800.left.bed ${breakpoint_directory}/D5.INV.2700.left.bed ${breakpoint_directory}/D5.INV.2600.left.bed ${breakpoint_directory}/D5.INV.2500.left.bed ${breakpoint_directory}/D5.INV.2400.left.bed ${breakpoint_directory}/D5.INV.2300.left.bed ${breakpoint_directory}/D5.INV.2200.left.bed ${breakpoint_directory}/D5.INV.2100.left.bed ${breakpoint_directory}/D5.INV.2000.left.bed ${breakpoint_directory}/D5.INV.1900.left.bed ${breakpoint_directory}/D5.INV.1800.left.bed ${breakpoint_directory}/D5.INV.1700.left.bed ${breakpoint_directory}/D5.INV.1600.left.bed ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed ${breakpoint_directory}/D5.INV.1600.right.bed ${breakpoint_directory}/D5.INV.1700.right.bed ${breakpoint_directory}/D5.INV.1800.right.bed ${breakpoint_directory}/D5.INV.1900.right.bed ${breakpoint_directory}/D5.INV.2000.right.bed ${breakpoint_directory}/D5.INV.2100.right.bed ${breakpoint_directory}/D5.INV.2200.right.bed ${breakpoint_directory}/D5.INV.2300.right.bed ${breakpoint_directory}/D5.INV.2400.right.bed ${breakpoint_directory}/D5.INV.2500.right.bed ${breakpoint_directory}/D5.INV.2600.right.bed ${breakpoint_directory}/D5.INV.2700.right.bed ${breakpoint_directory}/D5.INV.2800.right.bed ${breakpoint_directory}/D5.INV.2900.right.bed ${breakpoint_directory}/D5.INV.3000.right.bed ${breakpoint_directory}/D5.INV.3100.right.bed ${breakpoint_directory}/D5.INV.3200.right.bed ${breakpoint_directory}/D5.INV.3300.right.bed ${breakpoint_directory}/D5.INV.3400.right.bed ${breakpoint_directory}/D5.INV.3500.right.bed ${breakpoint_directory}/D5.INV.3600.right.bed ${breakpoint_directory}/D5.INV.3700.right.bed ${breakpoint_directory}/D5.INV.3800.right.bed ${breakpoint_directory}/D5.INV.3900.right.bed ${breakpoint_directory}/D5.INV.4000.right.bed ${breakpoint_directory}/D5.INV.4100.right.bed ${breakpoint_directory}/D5.INV.4200.right.bed ${breakpoint_directory}/D5.INV.4300.right.bed ${breakpoint_directory}/D5.INV.4400.right.bed ${breakpoint_directory}/D5.INV.4500.right.bed ${breakpoint_directory}/D5.INV.4600.right.bed ${breakpoint_directory}/D5.INV.4700.right.bed ${breakpoint_directory}/D5.INV.4800.right.bed ${breakpoint_directory}/D5.INV.4900.right.bed > ${sample_name}.INV.filtered.txt | |||
| # DUP | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1450.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1350.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1250.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1150.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1050.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.950.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.850.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.750.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.650.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.550.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.450.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.350.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.250.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.150.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.50.left.bed ${breakpoint_directory}/D5.DUP.50.right.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.150.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.250.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.350.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.450.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.550.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.650.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.750.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.850.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.950.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1050.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1150.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1250.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1350.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1450.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed > ${sample_name}.DUP.filtered.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1450.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1350.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1250.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1150.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1050.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.950.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.850.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.750.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.650.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.550.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.450.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.350.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.250.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.150.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.50.left.bed ${breakpoint_directory}/D5.DUP.50.right.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.150.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.250.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.350.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.450.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.550.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.650.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.750.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.850.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.950.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1050.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1150.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1250.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1350.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1450.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed > ${sample_name}.DUP.filtered.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DUP.4900.left.bed ${breakpoint_directory}/D5.DUP.4800.left.bed ${breakpoint_directory}/D5.DUP.4700.left.bed ${breakpoint_directory}/D5.DUP.4600.left.bed ${breakpoint_directory}/D5.DUP.4500.left.bed ${breakpoint_directory}/D5.DUP.4400.left.bed ${breakpoint_directory}/D5.DUP.4300.left.bed ${breakpoint_directory}/D5.DUP.4200.left.bed ${breakpoint_directory}/D5.DUP.4100.left.bed ${breakpoint_directory}/D5.DUP.4000.left.bed ${breakpoint_directory}/D5.DUP.3900.left.bed ${breakpoint_directory}/D5.DUP.3800.left.bed ${breakpoint_directory}/D5.DUP.3700.left.bed ${breakpoint_directory}/D5.DUP.3600.left.bed ${breakpoint_directory}/D5.DUP.3500.left.bed ${breakpoint_directory}/D5.DUP.3400.left.bed ${breakpoint_directory}/D5.DUP.3300.left.bed ${breakpoint_directory}/D5.DUP.3200.left.bed ${breakpoint_directory}/D5.DUP.3100.left.bed ${breakpoint_directory}/D5.DUP.3000.left.bed ${breakpoint_directory}/D5.DUP.2900.left.bed ${breakpoint_directory}/D5.DUP.2800.left.bed ${breakpoint_directory}/D5.DUP.2700.left.bed ${breakpoint_directory}/D5.DUP.2600.left.bed ${breakpoint_directory}/D5.DUP.2500.left.bed ${breakpoint_directory}/D5.DUP.2400.left.bed ${breakpoint_directory}/D5.DUP.2300.left.bed ${breakpoint_directory}/D5.DUP.2200.left.bed ${breakpoint_directory}/D5.DUP.2100.left.bed ${breakpoint_directory}/D5.DUP.2000.left.bed ${breakpoint_directory}/D5.DUP.1900.left.bed ${breakpoint_directory}/D5.DUP.1800.left.bed ${breakpoint_directory}/D5.DUP.1700.left.bed ${breakpoint_directory}/D5.DUP.1600.left.bed ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed ${breakpoint_directory}/D5.DUP.1600.right.bed ${breakpoint_directory}/D5.DUP.1700.right.bed ${breakpoint_directory}/D5.DUP.1800.right.bed ${breakpoint_directory}/D5.DUP.1900.right.bed ${breakpoint_directory}/D5.DUP.2000.right.bed ${breakpoint_directory}/D5.DUP.2100.right.bed ${breakpoint_directory}/D5.DUP.2200.right.bed ${breakpoint_directory}/D5.DUP.2300.right.bed ${breakpoint_directory}/D5.DUP.2400.right.bed ${breakpoint_directory}/D5.DUP.2500.right.bed ${breakpoint_directory}/D5.DUP.2600.right.bed ${breakpoint_directory}/D5.DUP.2700.right.bed ${breakpoint_directory}/D5.DUP.2800.right.bed ${breakpoint_directory}/D5.DUP.2900.right.bed ${breakpoint_directory}/D5.DUP.3000.right.bed ${breakpoint_directory}/D5.DUP.3100.right.bed ${breakpoint_directory}/D5.DUP.3200.right.bed ${breakpoint_directory}/D5.DUP.3300.right.bed ${breakpoint_directory}/D5.DUP.3400.right.bed ${breakpoint_directory}/D5.DUP.3500.right.bed ${breakpoint_directory}/D5.DUP.3600.right.bed ${breakpoint_directory}/D5.DUP.3700.right.bed ${breakpoint_directory}/D5.DUP.3800.right.bed ${breakpoint_directory}/D5.DUP.3900.right.bed ${breakpoint_directory}/D5.DUP.4000.right.bed ${breakpoint_directory}/D5.DUP.4100.right.bed ${breakpoint_directory}/D5.DUP.4200.right.bed ${breakpoint_directory}/D5.DUP.4300.right.bed ${breakpoint_directory}/D5.DUP.4400.right.bed ${breakpoint_directory}/D5.DUP.4500.right.bed ${breakpoint_directory}/D5.DUP.4600.right.bed ${breakpoint_directory}/D5.DUP.4700.right.bed ${breakpoint_directory}/D5.DUP.4800.right.bed ${breakpoint_directory}/D5.DUP.4900.right.bed > ${sample_name}.DUP.filtered.txt | |||
| # voted | |||
| # BND | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1450.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1350.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1250.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1150.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1050.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.950.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.850.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.750.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.650.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.550.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.450.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.350.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.250.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.150.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.50.left.bed ${breakpoint_directory}/D5.BND.50.right.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.150.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.250.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.350.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.450.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.550.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.650.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.750.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.850.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.950.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1050.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1150.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1250.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1350.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1450.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed > ${sample_name}.BND.voted.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1450.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1350.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1250.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1150.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1050.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.950.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.850.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.750.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.650.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.550.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.450.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.350.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.250.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.150.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.50.left.bed ${breakpoint_directory}/D5.BND.50.right.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.150.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.250.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.350.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.450.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.550.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.650.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.750.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.850.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.950.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1050.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1150.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1250.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1350.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1450.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed > ${sample_name}.BND.voted.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.BND.4900.left.bed ${breakpoint_directory}/D5.BND.4800.left.bed ${breakpoint_directory}/D5.BND.4700.left.bed ${breakpoint_directory}/D5.BND.4600.left.bed ${breakpoint_directory}/D5.BND.4500.left.bed ${breakpoint_directory}/D5.BND.4400.left.bed ${breakpoint_directory}/D5.BND.4300.left.bed ${breakpoint_directory}/D5.BND.4200.left.bed ${breakpoint_directory}/D5.BND.4100.left.bed ${breakpoint_directory}/D5.BND.4000.left.bed ${breakpoint_directory}/D5.BND.3900.left.bed ${breakpoint_directory}/D5.BND.3800.left.bed ${breakpoint_directory}/D5.BND.3700.left.bed ${breakpoint_directory}/D5.BND.3600.left.bed ${breakpoint_directory}/D5.BND.3500.left.bed ${breakpoint_directory}/D5.BND.3400.left.bed ${breakpoint_directory}/D5.BND.3300.left.bed ${breakpoint_directory}/D5.BND.3200.left.bed ${breakpoint_directory}/D5.BND.3100.left.bed ${breakpoint_directory}/D5.BND.3000.left.bed ${breakpoint_directory}/D5.BND.2900.left.bed ${breakpoint_directory}/D5.BND.2800.left.bed ${breakpoint_directory}/D5.BND.2700.left.bed ${breakpoint_directory}/D5.BND.2600.left.bed ${breakpoint_directory}/D5.BND.2500.left.bed ${breakpoint_directory}/D5.BND.2400.left.bed ${breakpoint_directory}/D5.BND.2300.left.bed ${breakpoint_directory}/D5.BND.2200.left.bed ${breakpoint_directory}/D5.BND.2100.left.bed ${breakpoint_directory}/D5.BND.2000.left.bed ${breakpoint_directory}/D5.BND.1900.left.bed ${breakpoint_directory}/D5.BND.1800.left.bed ${breakpoint_directory}/D5.BND.1700.left.bed ${breakpoint_directory}/D5.BND.1600.left.bed ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed ${breakpoint_directory}/D5.BND.1600.right.bed ${breakpoint_directory}/D5.BND.1700.right.bed ${breakpoint_directory}/D5.BND.1800.right.bed ${breakpoint_directory}/D5.BND.1900.right.bed ${breakpoint_directory}/D5.BND.2000.right.bed ${breakpoint_directory}/D5.BND.2100.right.bed ${breakpoint_directory}/D5.BND.2200.right.bed ${breakpoint_directory}/D5.BND.2300.right.bed ${breakpoint_directory}/D5.BND.2400.right.bed ${breakpoint_directory}/D5.BND.2500.right.bed ${breakpoint_directory}/D5.BND.2600.right.bed ${breakpoint_directory}/D5.BND.2700.right.bed ${breakpoint_directory}/D5.BND.2800.right.bed ${breakpoint_directory}/D5.BND.2900.right.bed ${breakpoint_directory}/D5.BND.3000.right.bed ${breakpoint_directory}/D5.BND.3100.right.bed ${breakpoint_directory}/D5.BND.3200.right.bed ${breakpoint_directory}/D5.BND.3300.right.bed ${breakpoint_directory}/D5.BND.3400.right.bed ${breakpoint_directory}/D5.BND.3500.right.bed ${breakpoint_directory}/D5.BND.3600.right.bed ${breakpoint_directory}/D5.BND.3700.right.bed ${breakpoint_directory}/D5.BND.3800.right.bed ${breakpoint_directory}/D5.BND.3900.right.bed ${breakpoint_directory}/D5.BND.4000.right.bed ${breakpoint_directory}/D5.BND.4100.right.bed ${breakpoint_directory}/D5.BND.4200.right.bed ${breakpoint_directory}/D5.BND.4300.right.bed ${breakpoint_directory}/D5.BND.4400.right.bed ${breakpoint_directory}/D5.BND.4500.right.bed ${breakpoint_directory}/D5.BND.4600.right.bed ${breakpoint_directory}/D5.BND.4700.right.bed ${breakpoint_directory}/D5.BND.4800.right.bed ${breakpoint_directory}/D5.BND.4900.right.bed > ${sample_name}.BND.voted.txt | |||
| # DEL | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1450.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1350.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1250.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1150.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1050.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.950.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.850.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.750.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.650.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.550.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.450.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.350.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.250.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.150.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.50.left.bed ${breakpoint_directory}/D5.DEL.50.right.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.150.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.250.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.350.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.450.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.550.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.650.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.750.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.850.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.950.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1050.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1150.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1250.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1350.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1450.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed > ${sample_name}.DEL.voted.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1450.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1350.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1250.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1150.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1050.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.950.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.850.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.750.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.650.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.550.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.450.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.350.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.250.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.150.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.50.left.bed ${breakpoint_directory}/D5.DEL.50.right.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.150.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.250.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.350.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.450.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.550.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.650.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.750.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.850.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.950.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1050.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1150.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1250.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1350.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1450.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed > ${sample_name}.DEL.voted.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DEL.4900.left.bed ${breakpoint_directory}/D5.DEL.4800.left.bed ${breakpoint_directory}/D5.DEL.4700.left.bed ${breakpoint_directory}/D5.DEL.4600.left.bed ${breakpoint_directory}/D5.DEL.4500.left.bed ${breakpoint_directory}/D5.DEL.4400.left.bed ${breakpoint_directory}/D5.DEL.4300.left.bed ${breakpoint_directory}/D5.DEL.4200.left.bed ${breakpoint_directory}/D5.DEL.4100.left.bed ${breakpoint_directory}/D5.DEL.4000.left.bed ${breakpoint_directory}/D5.DEL.3900.left.bed ${breakpoint_directory}/D5.DEL.3800.left.bed ${breakpoint_directory}/D5.DEL.3700.left.bed ${breakpoint_directory}/D5.DEL.3600.left.bed ${breakpoint_directory}/D5.DEL.3500.left.bed ${breakpoint_directory}/D5.DEL.3400.left.bed ${breakpoint_directory}/D5.DEL.3300.left.bed ${breakpoint_directory}/D5.DEL.3200.left.bed ${breakpoint_directory}/D5.DEL.3100.left.bed ${breakpoint_directory}/D5.DEL.3000.left.bed ${breakpoint_directory}/D5.DEL.2900.left.bed ${breakpoint_directory}/D5.DEL.2800.left.bed ${breakpoint_directory}/D5.DEL.2700.left.bed ${breakpoint_directory}/D5.DEL.2600.left.bed ${breakpoint_directory}/D5.DEL.2500.left.bed ${breakpoint_directory}/D5.DEL.2400.left.bed ${breakpoint_directory}/D5.DEL.2300.left.bed ${breakpoint_directory}/D5.DEL.2200.left.bed ${breakpoint_directory}/D5.DEL.2100.left.bed ${breakpoint_directory}/D5.DEL.2000.left.bed ${breakpoint_directory}/D5.DEL.1900.left.bed ${breakpoint_directory}/D5.DEL.1800.left.bed ${breakpoint_directory}/D5.DEL.1700.left.bed ${breakpoint_directory}/D5.DEL.1600.left.bed ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed ${breakpoint_directory}/D5.DEL.1600.right.bed ${breakpoint_directory}/D5.DEL.1700.right.bed ${breakpoint_directory}/D5.DEL.1800.right.bed ${breakpoint_directory}/D5.DEL.1900.right.bed ${breakpoint_directory}/D5.DEL.2000.right.bed ${breakpoint_directory}/D5.DEL.2100.right.bed ${breakpoint_directory}/D5.DEL.2200.right.bed ${breakpoint_directory}/D5.DEL.2300.right.bed ${breakpoint_directory}/D5.DEL.2400.right.bed ${breakpoint_directory}/D5.DEL.2500.right.bed ${breakpoint_directory}/D5.DEL.2600.right.bed ${breakpoint_directory}/D5.DEL.2700.right.bed ${breakpoint_directory}/D5.DEL.2800.right.bed ${breakpoint_directory}/D5.DEL.2900.right.bed ${breakpoint_directory}/D5.DEL.3000.right.bed ${breakpoint_directory}/D5.DEL.3100.right.bed ${breakpoint_directory}/D5.DEL.3200.right.bed ${breakpoint_directory}/D5.DEL.3300.right.bed ${breakpoint_directory}/D5.DEL.3400.right.bed ${breakpoint_directory}/D5.DEL.3500.right.bed ${breakpoint_directory}/D5.DEL.3600.right.bed ${breakpoint_directory}/D5.DEL.3700.right.bed ${breakpoint_directory}/D5.DEL.3800.right.bed ${breakpoint_directory}/D5.DEL.3900.right.bed ${breakpoint_directory}/D5.DEL.4000.right.bed ${breakpoint_directory}/D5.DEL.4100.right.bed ${breakpoint_directory}/D5.DEL.4200.right.bed ${breakpoint_directory}/D5.DEL.4300.right.bed ${breakpoint_directory}/D5.DEL.4400.right.bed ${breakpoint_directory}/D5.DEL.4500.right.bed ${breakpoint_directory}/D5.DEL.4600.right.bed ${breakpoint_directory}/D5.DEL.4700.right.bed ${breakpoint_directory}/D5.DEL.4800.right.bed ${breakpoint_directory}/D5.DEL.4900.right.bed > ${sample_name}.DEL.voted.txt | |||
| # INS | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1450.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1350.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1250.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1150.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1050.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.950.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.850.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.750.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.650.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.550.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.450.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.350.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.250.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.150.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.50.left.bed ${breakpoint_directory}/D5.INS.50.right.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.150.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.250.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.350.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.450.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.550.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.650.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.750.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.850.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.950.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1050.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1150.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1250.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1350.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1450.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed > ${sample_name}.INS.voted.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1450.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1350.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1250.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1150.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1050.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.950.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.850.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.750.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.650.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.550.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.450.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.350.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.250.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.150.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.50.left.bed ${breakpoint_directory}/D5.INS.50.right.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.150.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.250.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.350.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.450.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.550.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.650.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.750.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.850.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.950.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1050.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1150.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1250.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1350.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1450.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed > ${sample_name}.INS.voted.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INS.4900.left.bed ${breakpoint_directory}/D5.INS.4800.left.bed ${breakpoint_directory}/D5.INS.4700.left.bed ${breakpoint_directory}/D5.INS.4600.left.bed ${breakpoint_directory}/D5.INS.4500.left.bed ${breakpoint_directory}/D5.INS.4400.left.bed ${breakpoint_directory}/D5.INS.4300.left.bed ${breakpoint_directory}/D5.INS.4200.left.bed ${breakpoint_directory}/D5.INS.4100.left.bed ${breakpoint_directory}/D5.INS.4000.left.bed ${breakpoint_directory}/D5.INS.3900.left.bed ${breakpoint_directory}/D5.INS.3800.left.bed ${breakpoint_directory}/D5.INS.3700.left.bed ${breakpoint_directory}/D5.INS.3600.left.bed ${breakpoint_directory}/D5.INS.3500.left.bed ${breakpoint_directory}/D5.INS.3400.left.bed ${breakpoint_directory}/D5.INS.3300.left.bed ${breakpoint_directory}/D5.INS.3200.left.bed ${breakpoint_directory}/D5.INS.3100.left.bed ${breakpoint_directory}/D5.INS.3000.left.bed ${breakpoint_directory}/D5.INS.2900.left.bed ${breakpoint_directory}/D5.INS.2800.left.bed ${breakpoint_directory}/D5.INS.2700.left.bed ${breakpoint_directory}/D5.INS.2600.left.bed ${breakpoint_directory}/D5.INS.2500.left.bed ${breakpoint_directory}/D5.INS.2400.left.bed ${breakpoint_directory}/D5.INS.2300.left.bed ${breakpoint_directory}/D5.INS.2200.left.bed ${breakpoint_directory}/D5.INS.2100.left.bed ${breakpoint_directory}/D5.INS.2000.left.bed ${breakpoint_directory}/D5.INS.1900.left.bed ${breakpoint_directory}/D5.INS.1800.left.bed ${breakpoint_directory}/D5.INS.1700.left.bed ${breakpoint_directory}/D5.INS.1600.left.bed ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed ${breakpoint_directory}/D5.INS.1600.right.bed ${breakpoint_directory}/D5.INS.1700.right.bed ${breakpoint_directory}/D5.INS.1800.right.bed ${breakpoint_directory}/D5.INS.1900.right.bed ${breakpoint_directory}/D5.INS.2000.right.bed ${breakpoint_directory}/D5.INS.2100.right.bed ${breakpoint_directory}/D5.INS.2200.right.bed ${breakpoint_directory}/D5.INS.2300.right.bed ${breakpoint_directory}/D5.INS.2400.right.bed ${breakpoint_directory}/D5.INS.2500.right.bed ${breakpoint_directory}/D5.INS.2600.right.bed ${breakpoint_directory}/D5.INS.2700.right.bed ${breakpoint_directory}/D5.INS.2800.right.bed ${breakpoint_directory}/D5.INS.2900.right.bed ${breakpoint_directory}/D5.INS.3000.right.bed ${breakpoint_directory}/D5.INS.3100.right.bed ${breakpoint_directory}/D5.INS.3200.right.bed ${breakpoint_directory}/D5.INS.3300.right.bed ${breakpoint_directory}/D5.INS.3400.right.bed ${breakpoint_directory}/D5.INS.3500.right.bed ${breakpoint_directory}/D5.INS.3600.right.bed ${breakpoint_directory}/D5.INS.3700.right.bed ${breakpoint_directory}/D5.INS.3800.right.bed ${breakpoint_directory}/D5.INS.3900.right.bed ${breakpoint_directory}/D5.INS.4000.right.bed ${breakpoint_directory}/D5.INS.4100.right.bed ${breakpoint_directory}/D5.INS.4200.right.bed ${breakpoint_directory}/D5.INS.4300.right.bed ${breakpoint_directory}/D5.INS.4400.right.bed ${breakpoint_directory}/D5.INS.4500.right.bed ${breakpoint_directory}/D5.INS.4600.right.bed ${breakpoint_directory}/D5.INS.4700.right.bed ${breakpoint_directory}/D5.INS.4800.right.bed ${breakpoint_directory}/D5.INS.4900.right.bed > ${sample_name}.INS.voted.txt | |||
| # INV | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1450.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1350.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1250.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1150.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1050.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.950.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.850.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.750.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.650.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.550.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.450.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.350.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.250.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.150.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.50.left.bed ${breakpoint_directory}/D5.INV.50.right.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.150.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.250.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.350.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.450.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.550.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.650.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.750.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.850.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.950.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1050.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1150.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1250.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1350.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1450.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed > ${sample_name}.INV.voted.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1450.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1350.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1250.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1150.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1050.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.950.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.850.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.750.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.650.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.550.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.450.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.350.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.250.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.150.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.50.left.bed ${breakpoint_directory}/D5.INV.50.right.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.150.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.250.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.350.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.450.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.550.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.650.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.750.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.850.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.950.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1050.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1150.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1250.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1350.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1450.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed > ${sample_name}.INV.voted.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INV.4900.left.bed ${breakpoint_directory}/D5.INV.4800.left.bed ${breakpoint_directory}/D5.INV.4700.left.bed ${breakpoint_directory}/D5.INV.4600.left.bed ${breakpoint_directory}/D5.INV.4500.left.bed ${breakpoint_directory}/D5.INV.4400.left.bed ${breakpoint_directory}/D5.INV.4300.left.bed ${breakpoint_directory}/D5.INV.4200.left.bed ${breakpoint_directory}/D5.INV.4100.left.bed ${breakpoint_directory}/D5.INV.4000.left.bed ${breakpoint_directory}/D5.INV.3900.left.bed ${breakpoint_directory}/D5.INV.3800.left.bed ${breakpoint_directory}/D5.INV.3700.left.bed ${breakpoint_directory}/D5.INV.3600.left.bed ${breakpoint_directory}/D5.INV.3500.left.bed ${breakpoint_directory}/D5.INV.3400.left.bed ${breakpoint_directory}/D5.INV.3300.left.bed ${breakpoint_directory}/D5.INV.3200.left.bed ${breakpoint_directory}/D5.INV.3100.left.bed ${breakpoint_directory}/D5.INV.3000.left.bed ${breakpoint_directory}/D5.INV.2900.left.bed ${breakpoint_directory}/D5.INV.2800.left.bed ${breakpoint_directory}/D5.INV.2700.left.bed ${breakpoint_directory}/D5.INV.2600.left.bed ${breakpoint_directory}/D5.INV.2500.left.bed ${breakpoint_directory}/D5.INV.2400.left.bed ${breakpoint_directory}/D5.INV.2300.left.bed ${breakpoint_directory}/D5.INV.2200.left.bed ${breakpoint_directory}/D5.INV.2100.left.bed ${breakpoint_directory}/D5.INV.2000.left.bed ${breakpoint_directory}/D5.INV.1900.left.bed ${breakpoint_directory}/D5.INV.1800.left.bed ${breakpoint_directory}/D5.INV.1700.left.bed ${breakpoint_directory}/D5.INV.1600.left.bed ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed ${breakpoint_directory}/D5.INV.1600.right.bed ${breakpoint_directory}/D5.INV.1700.right.bed ${breakpoint_directory}/D5.INV.1800.right.bed ${breakpoint_directory}/D5.INV.1900.right.bed ${breakpoint_directory}/D5.INV.2000.right.bed ${breakpoint_directory}/D5.INV.2100.right.bed ${breakpoint_directory}/D5.INV.2200.right.bed ${breakpoint_directory}/D5.INV.2300.right.bed ${breakpoint_directory}/D5.INV.2400.right.bed ${breakpoint_directory}/D5.INV.2500.right.bed ${breakpoint_directory}/D5.INV.2600.right.bed ${breakpoint_directory}/D5.INV.2700.right.bed ${breakpoint_directory}/D5.INV.2800.right.bed ${breakpoint_directory}/D5.INV.2900.right.bed ${breakpoint_directory}/D5.INV.3000.right.bed ${breakpoint_directory}/D5.INV.3100.right.bed ${breakpoint_directory}/D5.INV.3200.right.bed ${breakpoint_directory}/D5.INV.3300.right.bed ${breakpoint_directory}/D5.INV.3400.right.bed ${breakpoint_directory}/D5.INV.3500.right.bed ${breakpoint_directory}/D5.INV.3600.right.bed ${breakpoint_directory}/D5.INV.3700.right.bed ${breakpoint_directory}/D5.INV.3800.right.bed ${breakpoint_directory}/D5.INV.3900.right.bed ${breakpoint_directory}/D5.INV.4000.right.bed ${breakpoint_directory}/D5.INV.4100.right.bed ${breakpoint_directory}/D5.INV.4200.right.bed ${breakpoint_directory}/D5.INV.4300.right.bed ${breakpoint_directory}/D5.INV.4400.right.bed ${breakpoint_directory}/D5.INV.4500.right.bed ${breakpoint_directory}/D5.INV.4600.right.bed ${breakpoint_directory}/D5.INV.4700.right.bed ${breakpoint_directory}/D5.INV.4800.right.bed ${breakpoint_directory}/D5.INV.4900.right.bed > ${sample_name}.INV.voted.txt | |||
| # DUP | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1450.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1350.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1250.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1150.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1050.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.950.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.850.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.750.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.650.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.550.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.450.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.350.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.250.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.150.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.50.left.bed ${breakpoint_directory}/D5.DUP.50.right.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.150.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.250.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.350.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.450.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.550.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.650.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.750.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.850.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.950.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1050.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1150.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1250.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1350.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1450.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed > ${sample_name}.DUP.voted.txt | |||
| # /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1450.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1350.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1250.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1150.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1050.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.950.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.850.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.750.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.650.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.550.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.450.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.350.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.250.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.150.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.50.left.bed ${breakpoint_directory}/D5.DUP.50.right.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.150.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.250.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.350.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.450.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.550.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.650.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.750.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.850.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.950.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1050.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1150.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1250.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1350.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1450.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed > ${sample_name}.DUP.voted.txt | |||
| /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DUP.4900.left.bed ${breakpoint_directory}/D5.DUP.4800.left.bed ${breakpoint_directory}/D5.DUP.4700.left.bed ${breakpoint_directory}/D5.DUP.4600.left.bed ${breakpoint_directory}/D5.DUP.4500.left.bed ${breakpoint_directory}/D5.DUP.4400.left.bed ${breakpoint_directory}/D5.DUP.4300.left.bed ${breakpoint_directory}/D5.DUP.4200.left.bed ${breakpoint_directory}/D5.DUP.4100.left.bed ${breakpoint_directory}/D5.DUP.4000.left.bed ${breakpoint_directory}/D5.DUP.3900.left.bed ${breakpoint_directory}/D5.DUP.3800.left.bed ${breakpoint_directory}/D5.DUP.3700.left.bed ${breakpoint_directory}/D5.DUP.3600.left.bed ${breakpoint_directory}/D5.DUP.3500.left.bed ${breakpoint_directory}/D5.DUP.3400.left.bed ${breakpoint_directory}/D5.DUP.3300.left.bed ${breakpoint_directory}/D5.DUP.3200.left.bed ${breakpoint_directory}/D5.DUP.3100.left.bed ${breakpoint_directory}/D5.DUP.3000.left.bed ${breakpoint_directory}/D5.DUP.2900.left.bed ${breakpoint_directory}/D5.DUP.2800.left.bed ${breakpoint_directory}/D5.DUP.2700.left.bed ${breakpoint_directory}/D5.DUP.2600.left.bed ${breakpoint_directory}/D5.DUP.2500.left.bed ${breakpoint_directory}/D5.DUP.2400.left.bed ${breakpoint_directory}/D5.DUP.2300.left.bed ${breakpoint_directory}/D5.DUP.2200.left.bed ${breakpoint_directory}/D5.DUP.2100.left.bed ${breakpoint_directory}/D5.DUP.2000.left.bed ${breakpoint_directory}/D5.DUP.1900.left.bed ${breakpoint_directory}/D5.DUP.1800.left.bed ${breakpoint_directory}/D5.DUP.1700.left.bed ${breakpoint_directory}/D5.DUP.1600.left.bed ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed ${breakpoint_directory}/D5.DUP.1600.right.bed ${breakpoint_directory}/D5.DUP.1700.right.bed ${breakpoint_directory}/D5.DUP.1800.right.bed ${breakpoint_directory}/D5.DUP.1900.right.bed ${breakpoint_directory}/D5.DUP.2000.right.bed ${breakpoint_directory}/D5.DUP.2100.right.bed ${breakpoint_directory}/D5.DUP.2200.right.bed ${breakpoint_directory}/D5.DUP.2300.right.bed ${breakpoint_directory}/D5.DUP.2400.right.bed ${breakpoint_directory}/D5.DUP.2500.right.bed ${breakpoint_directory}/D5.DUP.2600.right.bed ${breakpoint_directory}/D5.DUP.2700.right.bed ${breakpoint_directory}/D5.DUP.2800.right.bed ${breakpoint_directory}/D5.DUP.2900.right.bed ${breakpoint_directory}/D5.DUP.3000.right.bed ${breakpoint_directory}/D5.DUP.3100.right.bed ${breakpoint_directory}/D5.DUP.3200.right.bed ${breakpoint_directory}/D5.DUP.3300.right.bed ${breakpoint_directory}/D5.DUP.3400.right.bed ${breakpoint_directory}/D5.DUP.3500.right.bed ${breakpoint_directory}/D5.DUP.3600.right.bed ${breakpoint_directory}/D5.DUP.3700.right.bed ${breakpoint_directory}/D5.DUP.3800.right.bed ${breakpoint_directory}/D5.DUP.3900.right.bed ${breakpoint_directory}/D5.DUP.4000.right.bed ${breakpoint_directory}/D5.DUP.4100.right.bed ${breakpoint_directory}/D5.DUP.4200.right.bed ${breakpoint_directory}/D5.DUP.4300.right.bed ${breakpoint_directory}/D5.DUP.4400.right.bed ${breakpoint_directory}/D5.DUP.4500.right.bed ${breakpoint_directory}/D5.DUP.4600.right.bed ${breakpoint_directory}/D5.DUP.4700.right.bed ${breakpoint_directory}/D5.DUP.4800.right.bed ${breakpoint_directory}/D5.DUP.4900.right.bed > ${sample_name}.DUP.voted.txt | |||
| >>> | |||
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