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  • fabrice
    Member
    • Oct 2009
    • 86

    #1

    Is there any mature pipeline for DNA seq QC?

    For example, coverage, read depth, read quality and map quality etc
  • Baseless
    Member
    • Feb 2010
    • 31

    #2
    You could use fastqc for a quick evaluation of read quality, duplication levels and GC content.
    coverageBed from the Bedtools suite and a track file of your target regions is your friend regarding coverage analysis.
    And on enrichments, you might want to check out calculateHsMetrics from the picard tools suite to deterime if your enrichment was good and how many reads you got on/off target.
    Apart from that, I am not aware if there is a all-in-one solution.

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