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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.
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
DepthofCoverage log file.
Is the lower coverage in
CollectWgsMetrics due to the larger number of duplicated bases?
DepthofCoverage count duplicated reads differently?
Thanks a lot,