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How to remove non chromosome (1-22) from a .VCF file

Hi there, I am performing the GATK pipeline for converting fastq files to VCF format. How do I remove, non-chromosome 1-22 variants from the column of my VCF file obtained after the GATK variant recalibration step? The VCF snap shot is attached here. Any help is highly appreciated.

    GL000192.1      547218  .       C       T       93.26   PASS    AC=1;AF=0.011;AN=90;BaseQRankSum=-7.510e-01;DP=241;ExcessHet=3.0103;FS=0.000;GQ_MEAN=85.00;InbreedingCoeff=-0.0535;MLEAC=1;MLEAF=0.011;MQ=56.22;MQRankSum=0.589;NCC=0;NEGATIVE_TRAIN_SITE;QD=10.36;ReadPosRankSum=0.210;SOR=0.368;VQSLOD=-1.994e+00;culprit=MQRankSum     GT:AD:DP:GQ:PL  0/0:6,0:6:18:0,18,155   0/1:4,5:9:85:109,0,85   0/0:8,0:8:24:0,24,189   0/0:8,0:8:24:0,24,201   0/0:9,0:9:21:0,21,315   0/0:8,0:8:24:0,24,213        0/0:9,0:9:24:0,24,360   0/0:7,0:7:21:0,21,183   0/0:4,0:4:12:0,12,108   0/0:8,0:8:24:0,24,229   0/0:3,0:3:9:0,9,66      0/0:9,0:9:27:0,27,253        0/0:4,0:4:12:0,12,111   0/0:1,0:1:3:0,3,27      0/0:7,0:7:18:0,18,270   0/0:3,0:3:9:0,9,78      0/0:4,0:4:12:0,12,87    0/0:15,0:15:42:0,42,630      0/0:5,0:5:15:0,15,135   0/0:8,0:8:24:0,24,198   0/0:4,0:4:12:0,12,116   0/0:6,0:6:0:0,0,109     0/0:5,0:5:12:0,12,180   0/0:6,0:6:18:0,18,160   0/0:5,0:5:15:0,15,133        0/0:2,0:2:6:0,6,49      0/0:4,0:4:12:0,12,110   ./.:0,0:0:.:0,0,0       0/0:4,0:4:12:0,12,103   0/0:3,0:3:9:0,9,69      0/0:5,0:5:15:0,15,135        ./.:0,0:0:.:0,0,0       0/0:4,0:4:12:0,12,99    0/0:4,0:4:12:0,12,123   0/0:5,0:5:15:0,15,142   0/0:5,0:5:15:0,15,122   0/0:4,0:4:12:0,12,1130/0:2,0:2:6:0,6,49      0/0:4,0:4:12:0,12,124   0/0:3,0:3:9:0,9,84      0/0:6,0:6:18:0,18,150   0/0:8,0:8:18:0,18,270   0/0:1,0:1:3:0,3,29      0/0:3,0:3:9:0,9,66   0/0:4,0:4:12:0,12,105   0/0:5,0:5:15:0,15,114   0/0:4,0:4:0:0,0,49
GL000192.1      547235  .       C       G       244.16  PASS    AC=3;AF=0.034;AN=88;BaseQRankSum=-6.740e-01;DP=216;ExcessHet=0.0792;FS=0.000;GQ_MEAN=24.00;InbreedingCoeff=0.2294;MLEAC=3;MLEAF=0.034;MQ=54.98;MQRankSum=1.15;NCC=0;QD=20.35;ReadPosRankSum=-1.150e+00;SOR=0.495;VQSLOD=-2.486e+00;culprit=MQRankSum GT:AD:DP:GQ:PL       0/0:4,0:4:12:0,12,104   0/0:8,0:8:24:0,24,214   0/0:8,0:8:24:0,24,189   1/1:0,8:8:24:210,24,0   0/0:8,0:8:24:0,24,251   0/0:7,0:7:18:0,18,2700/0:7,0:7:18:0,18,270   0/0:7,0:7:21:0,21,183   0/0:4,0:4:0:0,0,49      0/0:7,0:7:21:0,21,209   0/0:2,0:2:6:0,6,46      0/0:10,0:10:30:0,30,282 0/0:5,0:5:15:0,15,134        ./.:0,0:0:.:0,0,0       0/0:7,0:7:21:0,21,217   0/0:3,0:3:9:0,9,78      0/0:4,0:4:12:0,12,86    0/0:13,0:13:39:0,39,371 0/0:5,0:5:15:0,15,148
chromosome removal
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written by jmukisa90 • jmukisa90

1 answer 

bcftools view --regions-file bed_file_containing_the_only_chromosomes_you_want.bed indexed.vcf.gz

or

bcftools view in.vcf | awk -F '\t' '($0 ~ /^#/ || $1 ~ /^(chr)?[0-9XY]+$/)'

or

bcftools view indexed.vcf.gz `cut -f 1 /path/to/ref.fa.fai | grep -E '^(chr)?[0-9XY]+$'`

or

....

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, Pierre, your code sorted me out well. Thanks.

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written by jmukisa90 • jmukisa90

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