The indel fraction is less than 20% but can be called in VCF as 50%

jjiangjjiang chinaMember
edited December 2016 in Ask the GATK team

Hi GATK team,

We used PCR amplicons to enrich the target genes, and sequence those targets with high depth, e.g., >1000X.
Followed with GATK best practice, we applied several steps to call the variants, except dedup and VQSR. We also applied UG caller instead of HC based on existed questions on GATK forum, to obtain relative ture calling.

I've came across a question that the heterozygosity of one deletion variant is less than 20%, but can be called at VCF using UG caller.
As displayed in IGV, the deletion coverage in this sample is 238, while A allele is 1191. Based on our parameter setup, this variant should not be call due to low indel fraction.
However, in VCF file, high quality calling was assigned to this variant, especially the AD info showed that there is 797 and 619 reads covered A and deletion alleles respectively, which made true calling for this variant.
17 41256089 rs373413425 AAAAAAAAAGAAAAG A 69575.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.180;DB;DP=1434;FS=0.000;MLEAC=1;MLEA F=0.500;MQ=61.21;MQ0=0;MQRankSum=7.931;QD=10.40;ReadPosRankSum=10.919;SOR=0.709 GT:AD:DP:GQ:PL 0/1:797,619:1412:99:69613,0,96385

I am wondering why? And can we get ABHet as SNP for Indel calling?

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