This adds a --vep_no_intergenic option to our PCGR wrapper. When specified, this feeds PCGR a modified TOML config file with the vep_skip_intergenic option enabled.
This reduces the number of variants processed downstream since PCGR filters out variants with no INFO/CSQ flag in the VEP'd input VCF.
This (hopefully) resolves #89 and resolves #91.
Fyi @ohofmann
-- Also removed Mutational Signature computation from PCGR, which will reduce computational time dramatically.
This adds a
--vep_no_intergenicoption to our PCGR wrapper. When specified, this feeds PCGR a modified TOML config file with thevep_skip_intergenicoption enabled. This reduces the number of variants processed downstream since PCGR filters out variants with noINFO/CSQflag in the VEP'd input VCF.This (hopefully) resolves #89 and resolves #91. Fyi @ohofmann
-- Also removed Mutational Signature computation from PCGR, which will reduce computational time dramatically.
(Also connected to umccr/vcf_stuff#3)