Is GATK overestimating the heterozygous calls?
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?
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.