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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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vcf2maf generates an empty maf file #353

Open Olsennnnn opened 5 months ago

Olsennnnn commented 5 months ago

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, likeWARNING: Couldn't retrieve bps around 26:16393 from reference FASTA: /home/data/my/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz. And there is no data in the generated maf file, only the table header, for example Hugo_Symbol,Entrez_Gene_Id,Center, etc Do you have any suggestion how to solve it? Thanks Olsen