Variant Allele Frequency
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9 months ago
adarsh_pp ▴ 10

How do we interpret the variant allele frequency to understand whether the variant is germline or somatic? How is it actually calculated?

I googled for these, but could not find a satisfactory answer.

Please help me, Thanks

Cancer • 444 views
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if you have a homogeneous tumor (without sub-clones) that is 100% pure (has no normal cells sequenced together) your allele frequency will be perfectly around 0.5 and 1 (OK this one is rare) - as for germline. In general (as Emily_Ensembl said) you need normal tissue and subtract normal mutations from tumor mutations.

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9 months ago
Emily 23k

A somatic variant is identified by calling the cancer tissue compared to a non-cancerous tissue. It has nothing to do with frequency.

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