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Picard CollectWgsMetrics for WES?


I want to get a coverage report for WES using Picard CollectWgsMetrics, since the DepthofCoverage function in GATK is relatively slow. But the coverage results differ a lot from the 2 programs.

* CollectWgsMetrics and DepthofCoverage wereprovided with the interval list file from the WES.
* ran with default settings.

CollectWgsMetrics reports mean coverage = 33.50, while DepthofCoverage reports 58.33. So I tried to find out why such big difference. I found that over 29.4% aligned bases were excluded in PCT_EXC_DUPE based on CollectWgsMetrics. However, only 8.9% of reads are filtered by DuplicateReadFilter in DepthofCoverage log file.

Is the lower coverage in CollectWgsMetrics due to the larger number of duplicated bases?

DoesCollectWgsMetrics and DepthofCoverage count duplicated reads differently?

Thanks a lot,


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