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vibansal / crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples
MIT License
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why can't find AF field for each sample #8

Closed Yiguan closed 5 years ago

Yiguan commented 5 years ago

the output VCF body: `

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A60_DSW65985-V_HTG27CCXY_L7_all A70_DSW65986-V_HTG27CCXY_L7_all

scf7180000003150|quiver 10520 . A G 301 LowDepth NP=2;DP=4,4,0;VT=SNV;CT=0.0;VP=1;VF=EMpass;AC=200;AF=0.99931;EMstats=30.17:-16.33;HWEstats=-0.0;MQS=0,0,0,9;FLANKSEQ=cggagtgaga:A:gattcgaact AC:GQ:DP:ADf:ADr:ADb .:12:7:0,4:0,2:0,0 .:12:2:0,0:0,2:0,0

scf7180000003150|quiver 10530 . T C 337 LowDepth NP=2;DP=3,5,1;VT=SNV;CT=0.0;VP=1;VF=EMpass;AC=200;AF=0.99947;EMstats=33.77:-16.72;HWEstats=-0.0;MQS=0,0,0,9;FLANKSEQ=agattcgaac:T:tccggcccct AC:GQ:DP:ADf:ADr:ADb .:13:7:0,3:0,3:0,0 .:13:2:0,0:0,2:0,0 "A60A70.vcf" 1544965L, 392577535C ` There are two samples, but AF field only appears in INFO, why can't I find AF in FORMAT for each sample?

vibansal commented 5 years ago

If you run with the --EM 0 option, you should get allele frequency for each sample.