ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.

[melodyeeeee]

Hi,
When I running this command :
`vcf2maf=/data/jiaf/wes_cancer/biosoft/vcf2maf/vcf2maf.pl
vep_path=~/miniconda3/envs/vep/bin/
GENOME=/data/jiaf/wes_cancer/biosoft/gsutil/gatk/hg19/v0/Homo_sapiens_assembly19.fasta
vep_data=/data/jiaf/wes_cancer/data/vep/homo_sapiens/100_GRCh37

cat config | while read id
do
arr=(${id})
tumor=${arr[0]}
perl ${vcf2maf}
--input-vcf filter/clean/${tumor}.clean.vcf
--output-maf annotation/vep/${tumor}_vep.maf
--ref-fasta ${GENOME}
--vep-path ${vep_path}
--vep-data ${vep_data}
--species homo_sapiens
--ncbi-build GRCh37
1>annotation/vep/${tumor}_vep.log 2>&1

done
And here is the error that I'm getting: [W::fai_fetch] Reference chr10:101563814-101563816 not found in FASTA file, returning empty sequence Failed to fetch sequence in chr10:101563814-101563816 ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. I tried to search the solution to get rid of it, and based on the https://github.com/mskcc/vcf2maf/issues/257, I have changed the fasta file to "chr" format and still get this issue, is there any other solution? my fastagrep "chr10" Homo_sapiens_assembly19.fasta
chr10 dna:chromosome chromosome:GRCh37:10:1:135534747:1`

Thank you!

[melodyeeeee]

I'm very sorry for the incorrect formatting, as this is the first time I've asked a question here, and would appreciate your understanding.

[chywang17]

Hi @melodyeeeee , I meet same problems. I wander know whether you have solved this issue.