systematically explore variant allele frequencies in combination with frameshifts

[dlaehnemann]

If you have a frameshift, a new open reading frame (ORF) is generated, with the frequency of the frameshift f as the new ORF frequency and 1 - f as the frequency of the original ORF. If a variant after that frameshift event has a frequency v that is larger than 1 - f, we know that the variant must be present in the frameshift ORF and in the original ORF. It must thus have happened before the frameshift was introduced and the frameshift ORF will have the variant at a frequency of 100% of f and the original ORF will have the variant with a frequency of v - f.

Possibly, more such clear-cut cases exist and can help eliminate some cases when dealing with frameshifts.