vcf2maf
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mskcc
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Hi all I have a VEP annotated vcf file. The annotation was done using VEP v103 with GRCh38 genome build. When I run the following code `perl vcf2maf.pl --input-vep 1880_somatic.filtered.VEP.vcf...
`--inhibit-vep` should not need to look for a FASTA file, but it does. ``` ERROR: Provided --ref-fasta is missing or empty: /users/dario/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.fa.gz ```
I have 77 vcfs, of which 73 are successfully converted to maf using vcf2maf.pl. The remaining 4 files reported `ERROR:Failed to run the VEP annotator` Here is the log of...
Hi, I have noticed that the commands posted are not supported by windows. For example, export, grep.. Is there a windows version? or what could I do to install this?...
Hi, I'm working with MAF files that were generated by another person from Caveman/Pindel calls and I'm trying to convert them to VCF files to work with another tool. For...
Hi， Thanks for developing this user-friendly tool for vcf2maf. When i finished running vcf2maf.pl, the output maf file was not complete. My code is : **perl vcf2maf.pl --input-vcf WES/QC/12.mutect2/Tumor_pass.vcf --output-maf...
I would like to find a match between a VCF and MAF file since I want to add some statistics (calculated from vcf file) per each site in the MAF...
i have recently tested out maf2vcf.pl: ``` perl /opt/maf2vcf.pl \\ --input-maf ${inputMaf} \\ --ref-fasta ${genomeFile} \\ --output-vcf test.vcf \\ --output-dir test ``` And I found that all my annotations were...
I've been using vcf2maf for a while, and just noticed while setting up a new computer that vcf2maf enforces the use of the ensembl-only vep cache (though this doesn't seem...
Hi, I want to convert my combined vcf file containing multiple samples to maf file. Can vcf2maf directly handle this? Thank you.
