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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!