The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.