It is recommended to run SetNmMdAndUqTags, and not necessary. #7191
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The sentence "... It is still necessary to subsequently run SetNmMdAndUqTags before running BQSR." has confused users on the forum. I believe that this step is actually optional, so please verify. Here is the forum post where the issue is raised. https://gatk.broadinstitute.org/hc/en-us/community/posts/360077484012-SetNmMdAndUqTags-is-mandatory-?page=1#community_comment_360014636751
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@jamesemery Could you please review this documentation update for accuracy? |
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This reverts commit f0b3447.
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This one got merged into the wrong branch (dc_markduplicatesspark_update_210408 instead of master) |
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Co-authored-by: Derek Caetano-Anollés <[email protected]>
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Replaced by #7535 |
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The sentence "... It is still necessary to subsequently run SetNmMdAndUqTags before running BQSR." has confused users on the forum. I believe that this step is actually optional, so please verify. Here is the forum post where the issue is raised.
https://gatk.broadinstitute.org/hc/en-us/community/posts/360077484012-SetNmMdAndUqTags-is-mandatory-?page=1#community_comment_360014636751