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CombineVariants resets AF to 0.5 and 1.0

Dear GATK Team,

I have been using CombineVariants to merge SNPs.vcf and Indels.vcf of the same sample into a single vcf file.

In the SNP.vcf and Indels.vcf files, I have changed the value for AF tag in INFO filed by calculating the 'actual frequency' from the AD tag.

So, when I merged the snp and indel vcf files, I expected the CombineVariants output vcf file to retain the 'actual frequency' that I calculated, but the tool CombineVariants has reset the values to 0.5 and 1.0

In the following example, the AF was set to 0.500 by HaplotypeCaller, I have used the AD tag values 50,29 to calculate the 'actual frequency' as 29/(50+29) = 0.367. And then I have changed the value of AF to 0.367.

VCF record with original AF value:
1 881627 rs2272757 G A 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582e+00;ClippingRankSum=-4.930e-01;DB;DP=79;ExcessHet=3.0103;FS=0.885;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=1.97;QD=5.79;ReadPosRankSum=2.70;SOR=0.906 GT:AD:DP:GQ:PL 0/1:50,29:79:99:486,0,1069

VCF record after re-calculating actual AF value:
1 881627 rs2272757 G A 457.77 . AC=1;AF=0.367;AN=2;BaseQRankSum=-1.582e+00;ClippingRankSum=-4.930e-01;DB;DP=79;ExcessHet=3.0103;FS=0.885;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=1.97;QD=5.79;ReadPosRankSum=2.70;SOR=0.906 GT:AD:DP:GQ:PL 0/1:50,29:79:99:486,0,1069

VCF record after merging files with CombineVariants :
1 881627 rs2272757 G A 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582e+00;ClippingRankSum=-4.930e-01;DB;DP=79;ExcessHet=3.0103;FS=0.885;MLEAC=1;MLEAF=0.500;MQ=59.83;MQRankSum=1.97;QD=5.79;ReadPosRankSum=2.70;SOR=0.906 GT:AD:DP:GQ:PL 0/1:50,29:79:99:486,0,1069

Is this the expected behavior of tool 'CombineVariants' that it resets AF value to 0.5 and 1.0 ?

Is there an option in CombineVariants that I can use to make this tool not reset the AF values ?

Thanks,
mglclinical

Issue · Github
by Sheila

Issue Number
1776
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

Best Answer

Answers

  • mglclinicalmglclinical USAMember

    @Sheila , than you for pointing me to VariantAnnotator

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