Showing docs for version 3.6-0 | The latest version is 4.1.4.0


AlleleBalanceBySample

Allele balance per sample

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)

Type ExperimentalAnnotation

Header definition line
  • FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele balance for each het genotype">

  • 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

    $$ AB = \frac{# REF reads from heterozygous samples}{# REF + ALT reads from heterozygous samples} $$

    Ideally, the value of AB should be close to 0.5, so half of the reads support the REF allele and half of the reads 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 in diploid organisms.
    • This annotation cannot currently be calculated for indels.
    • The 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 and normal contamination. 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.

    Related annotations


    Return to top


    See also GATK Documentation Index | Tool Docs Index | Support Forum

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