Default score threshold for PASS variants

[kiranchari]

Hi @sergeyvilov, there are no PASS or REJECT filters in DeepSom's output vcf file (final_predictions.vcf). What is the default score threshold you recommend for PASS variants? I need it to compute Tumor Mutation Burden for some samples.

[sergeyvilov]

Hi @kiranchari,
you should tune the threshold based on your needs. For example, you can look at DeepSom scores for mutations that are unlikely to be artefacts or germline mutations (e.g. mutations that you expect to see in patients suffering from a particular disease). Then you can set the threshold such that,say, 95% or 99% of these mutations are correctly identified by DeepSom as somatic.

[kiranchari]

Hi @sergeyvilov, that would require establishing some sort of ground-truth mutation set, which I don't have. I am also dealing with hundreds of samples, so I can't do that for each sample. Most callers usually provide some default thresholds for defining PASS variants..