AlleleBalanceBySample

Allele balance per sample

Category Variant Annotations

VCF Field FORMAT (sample genotype-level)

Type ExperimentalAnnotation

Header info
  • FORMAT=

  • Overview

    This is an experimental annotation that attempts to estimate whether the data supporting a heterozygous genotype call fits allelic ratio expectations, or whether there might be some bias in the data.

    Calculation

    $$ AB = \frac{# ALT alleles}{total # alleles} $$

    Ideally, the value of AB should be close to 0.5, so half of the alleles support the ref allele and half of the alleles support the alt allele. Divergence from the expected ratio may indicate that there is some bias in favor of one allele. Note the caveats below regarding cancer and RNAseq analysis.

    Caveats

    • This annotation will only work properly for biallelic heterozygous calls.
    • This annotation cannot currently be calculated for indels.
    • tThe reasoning underlying this annotation only applies to germline variants in DNA sequencing data. In somatic/cancer analysis, divergent ratios are expected due to tumor heterogeneity. In RNAseq analysis, divergent ratios may indicate differential allele expression.
    • As stated above, this annotation is experimental and should be interpreted with caution as we cannot guarantee that it is appropriate. Basically, use it at your own risk.

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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