Tumor Normal Filtering

[PedalheadPHX]

phoenix/utilities/variant_filtering.jst

Line 44 in 9f04da2

--exclude "{{ DB_exclude }}" \

This exclude line is not needed I believe:

The first filter is to get all the variants that are in COSMIC but would be filtered because that are in a public database (gnomAD, TOPMED). So there is not reason to have the DB_exclude

In the second filter we grab any variant that is not in the public databases, novel likely somatic events and rare inherited variants

Then these are merged to get the likely somatic candidates.