Is GATK overestimating the heterozygous calls?

Hi,
I have 24 genotypes distributed in 4 different populations.

I used HaplotypeCaller with the option –ERC –GVCF and obtained the vcf file for each genotype. Then combined all the genotypes to a single vcf file with GenotypeGVCFs option.

Is there a way to tell GATK to label a variant site as „Heterozygous“ only if it is present in >60% of the reads?

Example:
At position 82 (highlighted with a red box in the figure), the genotype field for this variant is 0/1. Whereas, as seen from the IGV, only 3 of the 10 reads contain an alternate allele „A“. Which filter should I use in the HaplotypeCaller or GenotypeGVCF or VariantFiltration to label a variant site as heterozygous if it’s present in say, for example 6 out of 10 reads.

Answers

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