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Roth-Lab / pyclone-vi

Fast method for inferring cancer clonal population structure from SNV data.
GNU General Public License v3.0
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How do I get variant_allele_frequency? #9

Closed TnakaNY closed 3 years ago

TnakaNY commented 3 years ago

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

TnakaNY commented 3 years ago

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?

aroth85 commented 3 years ago

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

TnakaNY commented 3 years ago

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.