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plz check my result from VariantAnnotator
gatk VariantAnnotator \ -R /path/to/human_g1k_v37_decoy.fasta \ -V trio_CGP.vcf \ -A PossibleDeNovo \ -A AlleleFraction \ -ped trio.ped \ -O trio_CGP_deno.vcf
I want annotate my vcf to add AF to each sample from command up.
But when I check my result:
1 865694 rs9988179 C T 4690.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=-2.670e-01;DB;DP=506;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;QD=10.04;ReadPosRankSum=1.76;SOR=0.703 GT:AD:AF:DP:GQ:JL:JP:PL:PP 0/1:132,109:0.434:241:99:94:94:2414,0,3163:2414,0,3223 0/0:39,0:0.434:39:94:94:94:0,94,1375:0,94,1375 0/1:128,98:0.434:226:99:94:94:2287,0,3139:2347,0,3139
PLZ attention! The last sample where AD=128,98,AF=0.434 is OK. But the first 2 samples' AFs are all 0.434. I check final vcf and find that all AFs in 3 samples are equal the last one. So, I think it is not correct.
plz check it!
gatk is 188.8.131.52 version