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Duplicates, flags, tallying and MultiQC report #50

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cerebis opened this issue Jul 2, 2021 · 0 comments

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cerebis commented Jul 2, 2021 •

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It has been asked that our MultiQC report contain the detected rate of duplication.

Further to this, we should ensure that qc3C respects BAM files where duplicates have already been marked. Tools such as GATK (picard) or samtools.

Are these reads flagged consistently?
Does qc3C count them to report a rate of duplication?
Double check that qc3C filters duplicate flagged reads (I am pretty certain it does).

cerebis added the enhancement label

cerebis changed the title ~~MultiQC report should contain duplication rate~~ Duplicates, flags, tallying and MultiQC report

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