DepthPerAlleleBySample

Depth of coverage of each allele per sample

Category Variant Annotations

VCF Field FORMAT (sample genotype-level)

Type StandardAnnotation

Header info
  • FORMAT=

  • Overview

    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.
    • For the AD calculation as performed by the UnifiedGenotyper, the same caveat as above applies to indels (but not to SNPs).
    • 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.
    • AlleleBallance is a generalization of this annotation over all samples.
    • AlleleBallanceBySample calculates allele balance for each individual sample.

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    See also Guide Index | Tool Documentation Index | Support Forum

    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA