Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
variants filtering VQSR
I ran VQSR with 30 samples and tranche filter level of 99.0 for both SNPs and INDELs. Around 82% of my variants call pass the filter. May I know is there any standard that can be used to evaluate how good the filtering result is?
Besides, if I split the gvcfs by chromosomes and run joint genotyping (GenotypeGVCFs) at chromosome level, is it going to affect the result compared to running at whole genome level?