vcf2maf
vcf2maf copied to clipboard
mskcc
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Hello, I'm trying to convert vcf file into MAF with vcf2maf, I have the environment with the packages installed, but whenever I try to convert a vcf file I got...
Hello, thanks for this great tool. We've been using it for years but I've noticed the latest release was in April 2021. Is it possible to release a new tag...
Thank you for developing this awsome tool. I would like to know what is the best practice for selecting a unique transcript based on vep2maf. I am in a clinical...
I installed VEP through `conda install -c bioconda ensembl-vep` . And my command for vcf2maf is `perl vcf2maf.pl --input-vcf 915.raw.somatic.vcf --output-maf 915.raw.somatic.maf --ref-fasta /storage/publicdata/ref/bwa/hg38_GATK/genome.fa --remap-chain /storage/lixuLab/suiyue/CHEK1/WES/clean_data/gatk/Separate/annovar/mskcc-vcf2maf-754d68a/data/hg38_to_GRCh38.chain --vep-path /home/lixuLab/suiyue/miniconda3/envs/WES/share/ensembl-vep-88.9-0` But I...
we are using vcf2maf prior to import to our local cBioPortal instance. We encounter a warning from cBioPortal's data validator that the MAF data contains Hugo Symbol:Entrez ID combinations that...
I found this flag while typing *vcf2maf --help*: -retain-fmt Comma-delimited names of FORMAT fields to retain as extra columns in MAF [] Unfortunately it doesn't work and it get an...
Hello, I tried running vcf2maf but got this error, would you mind helping me with this? Many thanks in advance! Best wishes, Kasit ``` perl vcf2maf/vcf2maf.pl --input-vcf /Users/kasit/Desktop/HN12-T-sample.b37-filtered.vcf --output-maf /Users/kasit/Desktop/HN12-T-sample.b37-filtered.maf...
Hi im traying to get some visual summaries from a vcf i annotated with VEP, and for that i want to use maftools but firts i have to get a...
Hi, While running `perl vcf2maf.pl --input-vcf newtest.vcf --output-maf test.vep.maf --vep-path /home/data/my/miniconda3/envs/vep/bin/ --vep-data /home/data/my/homo_sapiens/93_GRCh38/ --ref-fasta /home/data/my/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --ncbi-build GRCh38 --vep-forks 1`, I got a lot of warnings, like`WARNING: Couldn't retrieve bps around...
