vcf2maf rule creates vcfs/{patient}.vep.vcf file that should be accounted for as output.
Timing and memory needs to be extended for vep and vcf2maf. New time at least 45 minutes, new memory at least 16GB
vcf2maf FASTA should be ref_fasta used to align/call variants, not VEP fasta
See if the FASTA VEP uses can be removed or can be set up to use GATK reference used for variant calling - this may not be possible and will need a stack overflow question
vcf2maf looks like it annotates variants with VEP directly. If true, the vep rule is no longer needed and can be removed
Add reminder about how vcf2maf picks variants and possible need to change canonical transcripts
vcf2mafrule createsvcfs/{patient}.vep.vcffile that should be accounted for as output.vepandvcf2maf. New time at least 45 minutes, new memory at least 16GBvcf2mafFASTA should beref_fastaused to align/call variants, not VEP fastavcf2maflooks like it annotates variants with VEP directly. If true, theveprule is no longer needed and can be removedvcf2mafpicks variants and possible need to change canonical transcripts