fulcrumgenomics
question: need to correct MD/NM/UQ tags multiple times on piped commands or not?
Hi, I'm wondering if fgbio tools that modify reads (e.g. TrimPrimers, ClipBam) require correct MD/NM/UQ tags to function properly, and therefore they need to be correct prior to each call? So if several commands are piped in a row (e.g. TrimPrimers | ClipBam) they should be corrected at every step? Or is it safe to only correct them at the final step to save time? Thanks!
Related: specifying a reference for recalculating these tags is optional for TrimPrimers, but required for ClipBam. If correct tags aren't strictly required for the tools to operate properly, it would be nice to make it optional for ClipBam as well (with a warning in the doc) so that extra sorting isn't required (e.g. if tag correction will be performed downstream).
@eboyden would you be willing to sponsor some of this work to improve these tools?
I'm not opposed but I'm working on behalf of my company (Molecular Loop Biosciences) - I will bring it up. In the meantime please understand that these are questions and suggestions, not demands! If time doesn't allow working on them soon (or ever), I understand (and am grateful for this software being open source at all).
Will do. We're always looking for help improving our tools, whether that's from pull requests or sponsorship. If that's an option for your company, we'd be glad to chat: https://www.fulcrumgenomics.com/