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  • wangli
    Member
    • Apr 2012
    • 48
    #1

    how to account for the output of DepthOfCoverage in GATK

    Hi, all

    I want to check the mean depth of coverage of my bam file. The following is the content of the output file coverage.out.sample_summary:
    sample_id total mean granular_third_quartile granular_median granular_first_quartile %_bases_above_15
    FBK01 4282350373 10.58 1 1 1 8.2

    Does 10.58 account for the average depth of coverage? How to explain the %_bases_above_15? Does 15 mean the quality score? If so, 8.2% is too low.

    Thanks
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