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
I have vcf files which are generated using freebay, how could I add the clinvar annotation to the vcf and convert to maf? I try to run as following vep...
Hi, When I running this command : `vcf2maf=/data/jiaf/wes_cancer/biosoft/vcf2maf/vcf2maf.pl vep_path=~/miniconda3/envs/vep/bin/ GENOME=/data/jiaf/wes_cancer/biosoft/gsutil/gatk/hg19/v0/Homo_sapiens_assembly19.fasta vep_data=/data/jiaf/wes_cancer/data/vep/homo_sapiens/100_GRCh37 cat config | while read id do arr=(${id}) tumor=${arr[0]} perl ${vcf2maf} \ --input-vcf filter/clean/${tumor}.clean.vcf \ --output-maf annotation/vep/${tumor}_vep.maf \ --ref-fasta...
Hi, I have a kind of similar issue as in https://github.com/mskcc/vcf2maf/issues/332. I noticed this problem earlier and fixed the non matching names with previous data. Now I have the problem...
I am converting a VCF to MAF using the VCF2MAF program, and importing that into cbioportal. I notice that the "af" from the INFO field is not making to the...
Hi, I have run vcf2maf using vep 108, while the runs complete, it prints large number of warnings as following: ``` WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority! WARNING: Unrecognized...
Removes the `--af_esp` argument, which is deprecated in VEP 110, allowing maf2maf to run w/ VEP 110.
Hi, I am running vcf2maf installed from conda. I skip VEP, since I prepared the VEP annotated VCF with sarek (https://nf-co.re/sarek/3.2.1/usage). Here the VEP version used is 108. The problem...
Hi. I have trouble about the messages, like WARNING: Unrecognized effect "sequence_feature". Assigning lowest priority! when i run vcf2maf on my vcf file, i can see the messages all times....
Hi team Thanks for the great toolkit. I was wondering if this could be updated to work with later Ensembl vep releases (the latest as of Feb 2023 is 109.3...
Hi, I want the maf output to be annotated with COSV/COSM ids. but using the default options, the output was not annotated with cosmic ids. what is the command equivalent...
