Question: extract DP of heterozygotes from vcf file
0
gravatar for Ana
13 months ago by
Ana100
Ana100 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 13 months ago by Pierre Lindenbaum107k • written 13 months ago by Ana100
0
gravatar for mbk0asis
13 months ago by
mbk0asis320
Korea, Republic Of
mbk0asis320 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 13 months ago by mbk0asis320
0
gravatar for Pierre Lindenbaum
13 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum107k 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 13 months ago by Pierre Lindenbaum107k
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