Coverage

Total depth of coverage per sample and over all samples.

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

  • Overview

    This annotation is used to provide counts of read depth at two different levels, with some important differences. At the sample level (FORMAT), the DP value is the count of reads that passed the caller's internal quality control metrics (such as MAPQ > 17, for example). At the site level (INFO), the DP value is the unfiltered depth over all samples.

    See the method documentation on using coverage information for important interpretation details.

    Caveats

    • If downsampling is enabled (as is done by default for some analyses to remove excessive coverage), the depth of coverage effectively seen by the caller may be inferior to the actual depth of coverage in the original file. If using "-dcov D", the maximum depth that can be seen for N samples will be N * D.

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    GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.