These gVCFs were joint genotyped using GLnexus (https://www.biorxiv.org/content/10.1101/572347v1) to create a single, unfiltered project-level VCF (pVCF). Genotype depth filters (SNV DP≥7, indel DP≥10) were applied prior to variant site filters requiring at least one variant genotype passing an allele balance filter (heterozygous SNV AB>0.15, heterozygous indel<0.20), resulting in a second 'filtered' pVCF.
To maximize data utility and ease of use, an additional "Functionally Equivalent" (FE) pVCF was generated from FASTQs, following the primary analysis protocol described in the 2018 manuscript (PMID: 30279509) and then subject to GATK 3.0 variant calling and hard filtering of variants with inbreeding coefficient<-0.03 or without at least one variant genotype of DP≥10, GQ≥20 and, if heterozygous, AB≥0.20.
I am confusing to
1) heterozygous SNV AB>0.15, heterozygous indel<0.20 (I thought it should be heterozygous indel>0.20 )
2) if heterozygous, AB≥0.20 (without AB<=0.8, why?)
Thanks
