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cerebis / qc3C

Reference-free quality assessment for Hi-C sequencing data
GNU Affero General Public License v3.0
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Duplicates, flags, tallying and MultiQC report #50

Open cerebis opened 3 years ago

cerebis commented 3 years ago

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.

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