SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   how to account for the output of DepthOfCoverage in GATK (http://seqanswers.com/forums/showthread.php?t=21635)

wangli 07-12-2012 11:19 AM

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


All times are GMT -8. The time now is 03:51 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.