cat tier1.sv tier2.sv | grep DEL | cut -f1,2,5 | sed s'/END=//g' > SV.DEL
cat tier1.sv tier2.sv | grep DUP | cut -f1,2,5 | sed s'/END=//g' > SV.DUP

cat tier1.sv tier2.sv | grep INS | cut -f1,2 > SV.INS
cat SV.INS | awk '{print $1 "\t" ($2 - 500) "\t" ($2+500)}' | sort -k1,1 -k2,2n > sv.ins.break.point.500.bed

cat SV.DEL | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.del.break.point.left
cat SV.DEL | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.del.break.point.right
cat sv.del.break.point.left sv.del.break.point.right | sort -k1,1 -k2,2n > sv.del.break.point.500.bed

cat tier1.sv tier2.sv | grep TRA | grep -v 'chrM' | cut -f1,2,4,5  > SV.TRA
cat SV.TRA | awk '{print $1 "\t" ($2 - 500) "\t" ($2 + 500)}' > sv.tra.chr1
cat SV.TRA | cut -f3,4 | sed s'/CHR2=//g' | sed s'/END=//g' |awk '{print $1 "\t" ($2 - 500) "\t" ($2 + 500)}' > sv.tra.chr2
cat sv.tra.chr1 sv.tra.chr2 | sort -k1,1 -k2,2n > sv.tra.break.point.500.bed

cat tier1.sv tier2.sv | grep INV | cut -f1,2,5 | sed s'/END=//g' > SV.INV
cat SV.INV | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.inv.break.point.left
cat SV.INV | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.inv.break.point.right
cat sv.inv.break.point.left sv.inv.break.point.right | sort -k1,1 -k2,2n > sv.inv.break.point.500.bed

cat SV.DUP | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.dup.break.point.left
cat SV.DUP | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.dup.break.point.right
cat sv.dup.break.point.left sv.dup.break.point.right | grep -v 'chrM' | sort -k1,1 -k2,2n > sv.dup.break.point.500.bed



cat SV.INS | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.50
cat sv.ins.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.100
cat sv.ins.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.150
cat sv.ins.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.200
cat sv.ins.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.250
cat sv.ins.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.300
cat sv.ins.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.350
cat sv.ins.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.400

cat sv.ins.left.400 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.450
cat sv.ins.left.450 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.500
cat sv.ins.left.500 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.550
cat sv.ins.left.550 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.600
cat sv.ins.left.600 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.650
cat sv.ins.left.650 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.700
cat sv.ins.left.700 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.750
cat sv.ins.left.750 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.800
cat sv.ins.left.800 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.850
cat sv.ins.left.850 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.900
cat sv.ins.left.900 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.950
cat sv.ins.left.950 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1000
cat sv.ins.left.1000 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1050
cat sv.ins.left.1050 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1100
cat sv.ins.left.1100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1150
cat sv.ins.left.1150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1200
cat sv.ins.left.1200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1250
cat sv.ins.left.1250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1300
cat sv.ins.left.1300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1350
cat sv.ins.left.1350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1400
cat sv.ins.left.1400 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1450
cat sv.ins.left.1450 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1500




cat SV.INS | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.50
cat sv.ins.right.50 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.100
cat sv.ins.right.100 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.150
cat sv.ins.right.150 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.200
cat sv.ins.right.200 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.250
cat sv.ins.right.250 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.300
cat sv.ins.right.300 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.350
cat sv.ins.right.350 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.400

cat sv.ins.right.400 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.450
cat sv.ins.right.450 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.500
cat sv.ins.right.500 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.550
cat sv.ins.right.550 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.600
cat sv.ins.right.600 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.650
cat sv.ins.right.650 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.700
cat sv.ins.right.700 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.750
cat sv.ins.right.750 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.800
cat sv.ins.right.800 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.850
cat sv.ins.right.850 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.900
cat sv.ins.right.900 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.950
cat sv.ins.right.950 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.1000


















cat SV.DEL | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.50
cat sv.del.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.100
cat sv.del.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.150
cat sv.del.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.200
cat sv.del.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.250
cat sv.del.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.300
cat sv.del.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.350
cat sv.del.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.400


cat SV.DEL | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.50
cat sv.del.right.50 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.100
cat sv.del.right.100 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.150
cat sv.del.right.150 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.200
cat sv.del.right.200 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.250
cat sv.del.right.250 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.300
cat sv.del.right.300 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.350
cat sv.del.right.350 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.400




bedtools subtract -a GRCh38.bed -b diff.merged.bed > easy_region.bed


python /mnt/pgx_src_data_pool_4/home/renluyao/manuscript/SV/count_bed.py LCL5.high.confidence.bed

bedtools intersect -a LCL5.high.confidence.bed -b /mnt/pgx_src_data_pool_4/home/renluyao/Quartet/GIAB/NA12878_HG001/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed > LCL5.nist.common.bed
bedtools intersect -a LCL6.high.confidence.bed -b /mnt/pgx_src_data_pool_4/home/renluyao/Quartet/GIAB/NA12878_HG001/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed > LCL6.nist.common.bed
bedtools intersect -a LCL7.high.confidence.bed -b /mnt/pgx_src_data_pool_4/home/renluyao/Quartet/GIAB/NA12878_HG001/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed > LCL7.nist.common.bed
bedtools intersect -a LCL8.high.confidence.bed -b /mnt/pgx_src_data_pool_4/home/renluyao/Quartet/GIAB/NA12878_HG001/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed > LCL8.nist.common.bed

bedtools intersect -a LCL5.high.confidence.bed -b ensembl.bed  > LCL5.ensembl.bed

rtg vcffilter -i clinivar.chr.vcf.gz -o clinivar.chr.LCL5.vcf.gz --include-bed=LCL5.high.confidence.bed