ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build

[liuyang2006]

I encountered error below:

Script:

perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf  --ref-fasta $ref

Error message:

[W::fai_get_val] Reference 13:28608241-28608243 not found in FASTA file, returning empty sequence
[W::fai_get_val] Reference 13:28608241-28608243 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in 13:28608241-28608243
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.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 433.

[haghani-sara]

Hi, did you find out how to resolve this issue? I'm having the same problem

[sehaartuc]

Hi @haghani-sara , most probably you will need to check your VCF file and see the relevant fasta file at the beginning of your VCF. It should be in the first 10-12 row.