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DepthPerAlleleBySample

Depth of coverage of each allele per sample (AD)

Category Variant Annotations


Overview

Depth of coverage of each allele per sample

Also known as the allele depth, this annotation gives the unfiltered count of reads that support a given allele for an individual sample. The values in the field are ordered to match the order of alleles specified in the REF and ALT fields: REF, ALT1, ALT2 and so on if there are multiple ALT alleles.

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

Caveats

  • The AD calculation as performed by HaplotypeCaller may not yield exact results because only reads that statistically favor one allele over the other are counted. Due to this fact, the sum of AD may be different than the individual sample depth, especially when there are many non-informative reads.
  • Because the AD includes reads and bases that were filtered by the caller (and in case of indels, is based on a statistical computation), it should not be used to make assumptions about the genotype that it is associated with. Ultimately, the phred-scaled genotype likelihoods (PLs) are what determines the genotype calls.

Related annotations

  • Coverage gives the filtered depth of coverage for each sample and the unfiltered depth across all samples.

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GATK version 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.