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Normalized Coverage

IkerIker MadridMember

Hi all,

I'd like to know what is the definition for "normalized coverage" in "per target coverage" file calculated with PicardHsMetrics.

Thanks in advance.

Issue · Github
by Sheila

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  • deklingdekling Broad InstituteMember admin

    @Iker : We apologize for the delayed response. Normalized coverage in this context refers to relative coverage of a particular target interval with respect to the mean coverage of all of the target intervals. Essentially, for each target interval, the read depth (unique read starts) that correspond to a particular target interval is divided by the average number of read starts in all of the target intervals. This provides a metric to determine if specific target intervals have greater coverage than others. Variations in normalized coverage can result from differences in GC content, among other factors. Let us know if this explanation is not clear.

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