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Currently two flags (--udg) and (--udg_type) related to UDG treatment for downstream PMD/BamUtil trimming.
However functionally they pretty much do the same thing, but the latter being more detailed so you can condense into one.
It might also be worth modifying the flag name to --pmd_udg_type so a novice user doesn't add their UDG treatment when they don't in fact want PMD processing.
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The text was updated successfully, but these errors were encountered:
Currently two flags (--udg) and (--udg_type) related to UDG treatment for downstream PMD/BamUtil trimming.
However functionally they pretty much do the same thing, but the latter being more detailed so you can condense into one.
It might also be worth modifying the flag name to
--pmd_udg_type
so a novice user doesn't add their UDG treatment when they don't in fact want PMD processing.--
Sent from my mobile
The text was updated successfully, but these errors were encountered: