Somatic data

Somatic VCFs detected as somatic only (tumor minus normal) are analysed for mutational signatures

Allele Frequency

We do not import the AF value from the VCF, but instead [normalize](../vcf_samples.md#VCF Normalization) the data then recalculate AF to be AD / sum(AD for all variants at locus)

In an analysis, Sample, Cohort and Trio nodes can filter by allele frequency. For the Cohort and Trio nodes, all or any refers to requiring all samples to have allele frequency within the ranges or just one or more sample.

../_images/allele_frequency.png