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.
Effects of '--disable_indel_quals'
Apologies if this has been previously asked or explained elsewhere, but I could not find anything by searching.
We're hoping to reduce the size of our BAM files by including the '--disable_indel_quals' flag during the BQSR, but we're wondering:
1) if we're currently only interested in calling SNPs, will the lack of indel tags affect any of our downstream analyses?, and
2) if we eventually are interested in calling indels, could we rerun BQSR on the files created with '--disable_indel_quals' to obtain those indel tags?
Thank you in advance!