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plz check my result from VariantAnnotator

Polar_bearPolar_bear FreedomMember
edited November 2019 in Ask the GATK team
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 version

Best Answer


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