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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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traying to make a maf from an already annotated vcf #354

Open javierAPC opened 5 months ago

javierAPC commented 5 months ago

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 maf file, so i use this comand: perl vcf2maf.pl --input-vcf /home/victor/ensembl-vep/test_ann.vcf --output-maf tests/test.maf --tumor-id TUMOUR --normal-id NORMAL --inhibit-vep. which gives me this errors

[.......]
[W::fai_get_val] Reference chr10:101362827-101362833 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101362827-101362833
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410.

the thing is that for VEP i use the cache option (it didn't let me connect to the database) and the GRCh38 version of the human genome i have is in.vep/homo_sapiens/111_GRCh38, so i changed the vcf2maf.pl to point at that directory where i store Homo_sapiens.GRCh38.dna.toplevel.fa.gz. The vcf where also align to GRCh38.

Also before the test commands give this error ERROR: Provided --ref-fasta is missing or empty: /home/victor/.vep/homo_sapiens/102_GRCh37 but with the new reference give me this error:

[.......]
WARNING: Reference allele G at 7:116412043 doesn't match A (flanking bps: CAC) from reference FASTA: /home/victor/.vep/homo_sapiens/111_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
STATUS: Running VEP and writing to: tests/test.vep.vcf
ERROR: Cannot find VEP script under: /home/victor/miniconda3/bin

Uptade: cheking the reference in the header of the vcf, teh path is reference=/nfs-1-c1/work/d1/0034c2fad733d8de3f89c93ed42117/reference_files/genome.fa, again it should also be GRCh38