dsajdak
commented
2 months ago Hi @nsalgia - this isn't something that CCR needs to install as you can simply clone their Github repo and run the tool. Follow the directions under the Quick Start section. Then use perl to run the tool. I recommend loading CCR's perl module first with this command, then you can see their software just works:
$ module load gcc perl/5.34.0
$ perl vcf2maf.pl --man
NAME
vcf2maf.pl - Convert a VCF into a MAF by mapping each variant to only
one of all possible gene isoforms
SYNOPSIS
perl vcf2maf.pl --help
perl vcf2maf.pl --input-vcf INPUT.vcf --output-maf OUTPUT.maf --tumor-id TUMOR_ID --normal-id NORMAL_ID
DESCRIPTION
To convert a VCF into a MAF, each variant must be mapped to only one of
all possible gene transcripts/isoforms that it might affect. This
selection of a single effect per variant, is often subjective. This
project is an attempt to make the selection criteria smarter,
reproducible, and more configurable.
This script uses Ensembl's VEP, a variant annotator that maps effects of
a variant on all possible genes and transcripts. For more info, see the
README or <https://ensembl.org/info/docs/tools/vep/index.html>.
OPTIONS
--help Print a basic help message
--verbose
Print more things to STDERR to log progress
--input-vcf=*INPUT_VCF*
Path to input file in VCF format
If you run into any problems while trying this, please submit a support ticket to CCR Help. Thanks!
Hello,
We are hoping to install vcf2maf as a new module in CCR for analysis of DNA mutation calls. Here is the link to the github repository containing the package information: https://github.com/mskcc/vcf2maf
Please contact nicholas.salgia@roswellpark.org with any questions or if you need any additional information.
Thank you, Nick Salgia