extract DP of heterozygotes from vcf file

Question

[Ana]

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

Answer 1

[mbk0asis]

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

Answer 2

[Pierre Lindenbaum]

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]