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.
VQSR bundle based on b37 and hg19
Sorry to bother you guys. Just a few quick questions:
1) I'm attempting to download the bundles for VQSR and I noticed that they are for b37 or hg19. If I performed my initial assemblies and later SNP calls with hg38, will this cause an issue? Should I restart the process using either b37 or hg19?
2) I'm still a bit lost on what is considered "too few variants" for VQSR. As VQSR works best when there are thousands of variants - is this recommendation on a per sample basis or for an entire project? I'm presently working with sequences from 80 unique samples for a single gene (~100kbp) and HaplotypeCaller detects on average ~300 raw snps. Would you recommend I hard filter instead in my case?