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StrandAlleleCountsBySample

Number of forward and reverse reads that support each allele

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)

Header definition line
  • FORMAT=<ID=SAC,Number=.,Type=Integer,Description="Number of reads on the forward and reverse strand supporting each allele (including reference)">

  • Overview

    The StrandAlleleCountsBySample annotation produces read counts per allele (including (REF) and per strand. Note that, as with the AD annotation, the allele counts here should not be used to make assumptions about the called genotype.

    This annotation produces 2 values per allele at each site, corresponding to the number of reads that support the following (in that order):

    • the reference allele on the forward strand
    • the reference allele on the reverse strand
    • the first alternate allele on the forward strand
    • the first alternate allele on the reverse strand
    • the second alternate allele on the forward strand
    • ...etc

    Example

    GT:AD:GQ:PL:SB:SAC       1/2:1,18,12:99:1022,326,382,537,0,487:1,0,4,8:1,0,3,15,4,8

    In this example, the reference allele is supported by 1 read on the forward strand, the first alternate allele is supported by 3 forward and 15 reverse reads, and the second alternate allele is supported by 4 forward and 8 reverse reads.

    Caveats

    • This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator).

    Related annotations


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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.