How do I get variant_allele_frequency?

Question

Closed this issue 4 years ago · 3 comments

PyClone provides variant_allele_frequency value in its output file.
But, pyclone-vi does not have it in its output.

How do I calculate it?

To use pyclone-vi output for ClonEvol input, I need variant_allele_freq value.

Pyclone just uses below calculation?
VAF = AD / DP = Depth of Alt Allele / Total Depth

Answer 1 · 2021-01-20T20:27:07.000Z

I checked alt.count /(alt+ref count) vs pyclone.VAF. It is a bit different.
Is there any adjustment based on major/minor allele CNV in Pyclone?

Answer 2 · 2021-01-20T21:01:05.000Z

There should not be. If so it would be a bug :)

Answer 3 · 2021-01-21T00:45:21.000Z

I see. So, for pyclone-vi, I will add VAF (alt_allele/total depth) to the output by myself.

For future version, could you add VAF results in pyclone-vi output? It maybe easier for downstream analysis.