The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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!