I want to make sure I’m using the portal right. I basically want to get all the relevant processed data for a given patient ie PT_AJ04JZ0D … I’m not interested in improving upon the variant calls, so I just want the most processed/filtered results. I see there are a whole bunch of files listed as belonging to that patient’s tumor sample:
Where can I get info about what these are and which to use? I’m guessing that the one with consensus_somatic in its name is the one to use (and/or the corresponding maf).
And for the germline, I should just use the one called SL267368.hard-filtered.vcf.gz (annotated as “normal” tissue type)? Or should I use the gVCF file? I’d prefer not to have to download the gVCF files since they are so big.