Showing docs for version 3.7-0
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