search

Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
147 stars 43 forks source link

How we calculate VAF in scout #4686

Open northwestwitch opened 1 week ago

northwestwitch commented 1 week ago

We currently use the formula: alt reads / read depth but a user asked if we shouldn't instead use alt reads / (ref reads + alt reads).

Please note that the e formulas can return very different numbers, see for instance this variant: https://scout.scilifelab.se/cust087/F0062013/sv/variants/61a3b4da910ec616d0159eba2fbfed47

dnil commented 1 week ago

See also https://github.com/Clinical-Genomics/scout/issues/2920