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ERROR: Provided --ref-fasta is missing or empty #338

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medbenamine opened this issue Feb 14, 2023 · 3 comments
Closed

ERROR: Provided --ref-fasta is missing or empty #338

medbenamine opened this issue Feb 14, 2023 · 3 comments

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@medbenamine
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When I run this : vcf2maf-main]$ perl vcf2maf.pl --input-vcf /home/bendahm/s1.38.ann.vcf --output-maf s1.maf

I get this error :
ERROR: Provided --ref-fasta is missing or empty: /home/bendahm/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz

Any help, plz.
@complexgenome
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I get the same error.
Were you able to sort this?

@cameroncordero
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I am getting the same

@ckandoth
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You need to provide a path to a reference genome FASTA. By default, it points to $HOME/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz which is what you would have if you followed the instructions to install VEP and download the cache and reference genome.

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@ckandoth @complexgenome @cameroncordero @medbenamine