Extract inherited variants from VCF files in multiplex families

Question

[Crisr]

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

Answer 1

[Pierre Lindenbaum]

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