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Statistic TumorSampleAltAlleleFraction is truncated
Dear all,
This is not really an issue about the Strelka2 variant caller, but more a question about a particular statistic used in the algorithm:
I simply run Strelka2 (somatic mode) on a TCGA WES bam file (downsampled for an external purpose), and ask to output the variant statistics used in the machine learning algorithm (--reportEVSFeatures
).
The thing I don't understand is: why the variant allelic fraction of somatic calls (PASS and not PASS) are truncated? Maximum is 50%, see png file attached.
Does the algorithm re-scale this value?
Thanks in advance,
Tiffany
Note: I think it is not "truncated" but more re-scaled, i.e.
if TumorSampleAltAlleleFraction > 0.5 then TumorSampleAltAlleleFraction = 0.5
I found this piece of code which re-scales the AF to prevent for LOH regions. Does this have an influence on the interpretation of the final EVS score? See this post