The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?