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ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.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 this .vep/homo_sapiens/111_GRCh38), so i changed the vcf2maf.pl to pint at that directiry where i store Homo_sapiens.GRCh38.dna.toplevel.fa.gz. The vcf where also alignt with 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
