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
ExAC allele counts and frequencies are already in the VEP cache. But we use the `ExAC_nonTCGA` VCF instead, minus a few known somatic variants related to hematopoietic clonal expansion. Figure...
 Can you update the guide of download VEP database? and I want to ask why ref that used in maf2vcf is GRCR_37 ?
`vcf2maf.pl` annotates this as ``` Hugo_Symbol Entrez_Gene_Id PRAMEF5 645359 ``` But PRAMEF5 has entrez gene id: 343068, and 645359 is actually PRAMEF26. What is happening here?
I have a vcf file which have few rows with following type of data and I could observe that all of this is being filtered out. ``` grep -v "^#"...
Hi, Long time I am trying vcf2maf; It runs ok with test data but with my vcf I am getting error ``` -bash-4.1$ perl vcf2maf.pl --input-vcf /temp/hgig/fi1d18/strelka-2.9.2.centos6_x86_64/bin/demo_somatic_036_2post/results/variants/double_filtered_somatic_036_2post.snvs.vcf --output-maf tests/test.vep.maf --filter-vcf...
Is it possible to run vcf2maf using the (offline) vep synonyms.txt file for chromosome synonyms? Is there an option to allow this set of options when generating the vep-annotated vcf...
Hi ckandoth, I tried the updated Dockerfile but it didn't build. Can you please look into it? ! Installing the dependencies failed: Module 'XML::LibXML' is not installed, Module 'XML::LibXML::Reader' is...
To what fields does the info from the INFO field SOMATIC on a VCF translate to on a MAF file (I believe the SOMATIC column in MAF does not actually...
Hello. Mac OS x El Capitan 10.11.6. After installing pre-reqs (VEP and samtools) and vcf2maf I got to the test step in the manual and got this error: $ perl...
Hello, I applied `vcf2maf` to a vcf file cleaned with `vcf2vcf`. The original vcf was an output from `pindel`. I have the following error from running `vcf2maf`. Would you please...
