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SV_MIE/codescripts/get_sv_region.sh

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Originale Blame Cronologia 

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

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

  3. 

  4. cat tier1.sv tier2.sv | grep INS | cut -f1,2 > SV.INS

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

  6. 

  7. cat SV.DEL | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.del.break.point.left

  8. cat SV.DEL | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.del.break.point.right

  9. cat sv.del.break.point.left sv.del.break.point.right | sort -k1,1 -k2,2n > sv.del.break.point.500.bed

  10. 

  11. cat tier1.sv tier2.sv | grep TRA | grep -v 'chrM' | cut -f1,2,4,5  > SV.TRA

  12. cat SV.TRA | awk '{print $1 "\t" ($2 - 500) "\t" ($2 + 500)}' > sv.tra.chr1

  13. 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

  14. cat sv.tra.chr1 sv.tra.chr2 | sort -k1,1 -k2,2n > sv.tra.break.point.500.bed

  15. 

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

  17. cat SV.INV | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.inv.break.point.left

  18. cat SV.INV | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.inv.break.point.right

  19. cat sv.inv.break.point.left sv.inv.break.point.right | sort -k1,1 -k2,2n > sv.inv.break.point.500.bed

  20. 

  21. cat SV.DUP | awk '{print $1 "\t" ($2 - 500) "\t" $2}'  > sv.dup.break.point.left

  22. cat SV.DUP | awk '{print $1 "\t" $3 "\t" ($3 + 500)}'  > sv.dup.break.point.right

  23. 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

  24. 

  25. 

  26. 

  27. cat SV.INS | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.50

  28. cat sv.ins.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.100

  29. cat sv.ins.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.150

  30. cat sv.ins.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.200

  31. cat sv.ins.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.250

  32. cat sv.ins.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.300

  33. cat sv.ins.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.350

  34. cat sv.ins.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.400

  35. 

  36. cat sv.ins.left.400 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.450

  37. cat sv.ins.left.450 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.500

  38. cat sv.ins.left.500 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.550

  39. cat sv.ins.left.550 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.600

  40. cat sv.ins.left.600 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.650

  41. cat sv.ins.left.650 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.700

  42. cat sv.ins.left.700 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.750

  43. cat sv.ins.left.750 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.800

  44. cat sv.ins.left.800 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.850

  45. cat sv.ins.left.850 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.900

  46. cat sv.ins.left.900 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.950

  47. cat sv.ins.left.950 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1000

  48. cat sv.ins.left.1000 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1050

  49. cat sv.ins.left.1050 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1100

  50. cat sv.ins.left.1100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1150

  51. cat sv.ins.left.1150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1200

  52. cat sv.ins.left.1200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1250

  53. cat sv.ins.left.1250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1300

  54. cat sv.ins.left.1300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1350

  55. cat sv.ins.left.1350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1400

  56. cat sv.ins.left.1400 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1450

  57. cat sv.ins.left.1450 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.ins.left.1500

  58. 

  59. 

  60. 

  61. 

  62. cat SV.INS | awk '{print $1"\t"$2 "\t" ($2 + 50)}' > sv.ins.right.50

  63. cat sv.ins.right.50 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.100

  64. cat sv.ins.right.100 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.150

  65. cat sv.ins.right.150 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.200

  66. cat sv.ins.right.200 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.250

  67. cat sv.ins.right.250 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.300

  68. cat sv.ins.right.300 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.350

  69. cat sv.ins.right.350 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.400

  70. 

  71. cat sv.ins.right.400 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.450

  72. cat sv.ins.right.450 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.500

  73. cat sv.ins.right.500 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.550

  74. cat sv.ins.right.550 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.600

  75. cat sv.ins.right.600 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.650

  76. cat sv.ins.right.650 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.700

  77. cat sv.ins.right.700 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.750

  78. cat sv.ins.right.750 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.800

  79. cat sv.ins.right.800 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.850

  80. cat sv.ins.right.850 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.900

  81. cat sv.ins.right.900 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.950

  82. cat sv.ins.right.950 | awk '{print $1"\t"$3 "\t" ($3 + 50)}' > sv.ins.right.1000

  83. 

  84. 

  85. 

  86. 

  87. 

  88. 

  89. 

  90. 

  91. 

  92. 

  93. 

  94. 

  95. 

  96. 

  97. 

  98. 

  99. 

  100. 

  101. cat SV.DEL | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.50

  102. cat sv.del.left.50 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.100

  103. cat sv.del.left.100 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.150

  104. cat sv.del.left.150 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.200

  105. cat sv.del.left.200 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.250

  106. cat sv.del.left.250 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.300

  107. cat sv.del.left.300 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.350

  108. cat sv.del.left.350 | awk '{print $1 "\t" ($2 - 50) "\t" $2}' > sv.del.left.400

  109. 

  110. 

  111. cat SV.DEL | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.50

  112. cat sv.del.right.50 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.100

  113. cat sv.del.right.100 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.150

  114. cat sv.del.right.150 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.200

  115. cat sv.del.right.200 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.250

  116. cat sv.del.right.250 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.300

  117. cat sv.del.right.300 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.350

  118. cat sv.del.right.350 | awk '{print $1 "\t" $3 "\t" ($3 + 50)}' > sv.del.right.400

  119. 

  120. 

  121. 

  122. 

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

  124. 

  125. 

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

  127. 

  128. 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

  129. 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

  130. 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

  131. 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

  132. 

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

  134. 

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

  136. 

  137. 

  138. 

  139.