Extract inherited variants from VCF files in multiplex families
I have experience with extracting de novo variants in trios, but I am not sure if there is any tool to extract the inherited variants from vcf files in multiplex families The header is and one line as example:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT EA1 EA2 EA3 EA4 M P
1 13116 . T G 17852.6 PASS AC=6;AF=0.5;AN=12;BaseQRankSum=-0.14;DP=659;ExcessHet=14.6052;FS=9.274;MLEAC=6;MLEAF=0.5;MQ=28.96;MQRankSum=-5.711;QD=27.17;ReadPosRankSum=-0.077;SOR=1.326 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:54,68:122:99:0|1:13116_T_G:2649,0,2035:13116 0/1:15,92:107:99:0|1:13110_G_A:3796,0,349:13110 0/0:27,100:127:99:0|1:13116_T_G:4047,0,825:13116 0/0:45,74:119:99:0|1:13116_T_G:2922,0,1646:13116 0/1:27,46:73:99:0|1:13110_G_A:1825,0,995:13110 0/0:41,68:109:99:0|1:13116_T_G:2621,0,1491:13116
My difficulty is given by all the possible combination in the genotypes and how would be possible to extract them. In this case the father trasmitted the allele to the EA1 child. But how can I get all the possible trasmitted alleles across the vcf? Thank you very much Best Cris
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Pierre Lindenbaum
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Crisr •
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Crisr •
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using vcffilterjdk http://lindenb.github.io/jvarkit/VcfFilterJdk.html
check father "S2" and children "S3" share at least one common ALT allele.
java -jar ${JVARKIT_DIST}/vcffilterjdk.jar -e 'final Genotype fG= variant.getGenotype("S2"); final Genotype cG = variant.getGenotype("S3"); final Set<Allele> fA= fG.getAlleles().stream().filter(G->!(G.isNoCall() || G.isReference())).collect(Collectors.toSet()); return !fA.isEmpty() && cG.getAlleles().stream().anyMatch(A->fA.contains(A));' in.vcf
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