About allele balance

Am i available to obtain the data of allele frequency for homozygotes? I’m interested in SNV 9-77797578-G-A (GRCh38), which may cause Sturge Weber Syndrome. Nevertheless, I want to get the proportion of how many alleles frequencies are smaller than 1% and 0.25%.

Just to clarify, the so called allele frequency i need is the mutant allele frequency, which is the number of mutant reads / total number of reads at one specific position for one sample. I guess it’s the allele balance shown in gnomAD.

Hi @Ruizhe_Zhang,

We do not calculate homozygous reference samples allele balance as we work off of a hail VDS file which only contains a single allele depth value for hom-ref samples (DP) and thus we do not have any read information for any alternate reads at these entries.