Any change on the recommendation for genotype-based QC for GVCF called variants?
For QC, we have an old practice of setting low quality genotypes with low DP and/or GQ to missing, e.g. DP<8 and GQ<20.
We noticed that, for the variants called from the GVCF files using HaplotypeCaller, those parameters of homozygous reference (0/0) no longer represent the variant itself but the whole non-var block of the individual. e.g. DP reflects MIN_DP of the non-var block (as far as we see), so as GQ.
May I know that if it is still advisable to do this kind of genotype-based QC based on GQ and DP? or how would you advise for further QC, besides VQSR? This would affect quite a lot on protocol for discovering de novo variants.