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
This flag stops vcf2maf from running with vep 107 (haven't tested it for earlier versions)
duplicate #229 , because it doesn't have answer I have txt and html file from vep How can I use it for vcf2maf?
Hello everyone! I'm trying to run VCF after sucessfully using VEP. When I use: ` vcf2maf --input-vcf /home/gabriel.gama/Mutect2_usingPoN/sample11_withPoN.vcf --output-maf /home/gabriel.gama/Mutect2_usingPoN/sample11_vcf2maf.vep.maf --ref-fasta /home/gabriel.gama/references/ENSEMBL/star/Homo_sapiens.GRCh38.dna.primary_assembly.fa ` I'm getting: ` STATUS: Running VEP and...
I have a problem with VEP it seems. Complaining about Unknown option: af_gnomad perl ~/software/vcf2maf-1.6.21/vcf2maf.pl --ref-fasta /home/local/xxxx/.vep/homo_sapiens/102_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --input-vcf PANCNGS-006.vcf --output-maf PANCNGS-006.vcf.maf --tumor-id T-PANCNGS-006 --normal-id N-PANCNGS-006 --vep-path /home/local/xxxx/anaconda3/bin STATUS: Running VEP...
Hi, we're using older version (1.6.17) of vcf2maf and recently it choked on a vcf with line (I zeroed out the exact locus) 13 32900000 NM_000059.3:c.0000-000_*1500000del G . PASS;EXT "END=34400000;SVTYPE=DEL;SVLEN=1500000;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=C";ANN=|upstream_gene_variant........
Per https://github.com/Ensembl/ensembl-vep/releases/tag/release%2F105.0 there are 3 new effect terms in VEP that need handling. - splice_donor_5th_base_variant (SO:0001787) - splice_donor_region_variant (SO:0002170) - splice_polypyrimidine_tract_variant (SO:0002169) I set the priority to match splice_region_variant (see...
I've noticed in my last two runs of maf2maf that `n_alt_count` and `n_ref_count` can be altered during reannotation by `maf2maf.pl`. This occurs when a variant is present in multiple samples....
$ perl vcf2maf.pl --input-vcf xxx.snp.vcf --output-maf test.maf --ref-fasta ../pig.dna.toplevel.fa STATUS: Running VEP and writing to: xxx.snp.vep.vcf ERROR: Cannot find VEP script under: /yyy/miniconda3/bin
The dockerized command and outputs, along with dstat lines (set one entry per 10 minutes during the run) on a 36 threaded computer. With "--vep-forks 45", the observation is ~23...
