Question: extract DP of heterozygotes from vcf file
0
gravatar for Ana
4 weeks ago by
Ana0
Ana0 wrote:

Hi everyone

I want to plot the read distribution only in heterozygote genotypes in my vcf file. Does anyone has any idea how to extract only DP values of heterozygotes? Thanks

ADD COMMENTlink modified 4 weeks ago by Pierre Lindenbaum93k • written 4 weeks ago by Ana0
0
gravatar for mbk0asis
4 weeks ago by
mbk0asis200
Korea, Republic Of
mbk0asis200 wrote:

try

grep -Po 'DP=.*' INPUT | cut -d";" -f1

INPUT

chrX    129 .   G   GT,GGT  27173.73    .   AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=2.721;ClippingRankSum=-0.400;DP=2555;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.46;MQRankSum=-3.139;QD=27.54;ReadPosRankSum=-1.613;SOR=2.163   GT:AD:DP:GQ:PL  1/2:20,98,322:440:99:27211,8108,6549,2362,0,549
chrX    225 .   T   TC,TTGGGC   2133.73 .   AC=1,1;AF=0.500,0.500;AN=2;DP=930;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.47;QD=29.39;SOR=2.124 GT:AD:DP:GQ:PL  1/2:0,23,9:32:99:2171,378,207,767,0,744

OUTPUT

DP=2555
DP=930
ADD COMMENTlink written 4 weeks ago by mbk0asis200
0
gravatar for Pierre Lindenbaum
4 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum93k wrote:

Using bioalcidae: https://github.com/lindenb/jvarkit/wiki/BioAlcidae

$ java -jar dist/bioalcidae.jar -e 'while(iter.hasNext()) { var vc=iter.next(),i=0;for(i=0;i< vc.getNSamples();++i) { var g=vc.getGenotype(i); if(!g.isHet()) continue; out.println(vc.getContig()+" "+vc.getStart()+" "+g.getSampleName()+" "+g.getDP()+" "+g.getAlleles());}}' in.vcf



1 1149835 Sample1 1042 [A*, G]
1 1149973 Sample1 531 [C*, A]
1 1152069 Sample1 31 [A*, ATGAGACCGCACCAGCGTGTC]
1 1152369 Sample1 272 [G*, A]
1 1152369 Sample2 65 [G*, A]
1 1152431 Sample1 298 [A*, G]
1 1152689 Sample2 16 [C*, A]
1 1152689 Sample3 9 [C*, A]
1 1152689 Sample4 11 [C*, A]
1 1152689 Sample5 [C*, A]
ADD COMMENTlink written 4 weeks ago by Pierre Lindenbaum93k
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