Showing docs for version 3.7-0

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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">

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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.

Related annotations

• DepthPerAlleleBySample calculates depth of coverage for each allele per sample (AD).
• DepthPerSampleHC calculates depth of coverage after filtering by HaplotypeCaller.

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