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question: need to correct MD/NM/UQ tags multiple times on piped commands or not? #877

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@eboyden

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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!

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