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CombineVariants: GT field is not updated when merging variants with different ALT alleles

sbahetisbaheti Posts: 18Member
edited September 2013 in Ask the GATK team


my two VCF files have different alternate allele at the same position as i have called the variants using two different callers. When i run combine Variants on the both my GT field is not updated properly. AD field is also not updated properly but i ran Variant Annotator and that fixes that issue.

VCF 1:

chr1    87708015    rs58006838  C   T   145.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.479;DB;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;QD=10.41;ReadPosRankSum=0.925  GT:AD:DP:GQ:PL  0/1:3,9:14:37:174,0,37

VCF 2:

chr1    87708015    .   C   A   .   PASS    AN=2;DP=4;NS=1  GT:AD:DP:GQ 0/1:2,2:4:8.42

Merged VCF file:

chr1    87708015    rs58006838  C   T,A 145.77  PASS    AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.479;DB;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;NS=1;QD=10.41;ReadPosRankSum=0.925;set=Intersection GT:AD:DP:GQ **0/1**:3,9,2:14:37

command used:

java -jar $gatk/2.7-1-g42d771f/GenomeAnalysisTK.jar -T CombineVariants -V one.vcf.gz -V two.vcf.gz -o test.vcf -R $ref

Is this a known limitation or a bug?

Post edited by Geraldine_VdAuwera on


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