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Old 07-12-2012, 10:19 AM   #1
wangli
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Location: Texas

Join Date: Apr 2012
Posts: 48
Default 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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