Unable to find FASTA index entry for '1'

Question

[ja4123]

Hey, I have a sorted and indexed .bam file, and I am running it through freebayes, with the script :

freebayes -f ref.fa -@ in.vcf.gz aln.bam >var.vcf

very time I run this script I get the:

unable to find FASTA index entry for '1'

Even know I have the index files.

I have the correct Bam file (downloaded from here: https://www.internationalgenome.org/data-portal/sample/NA12878) and index files and it just continually throws the indexing error. What could be the problem here?

Answer 1

[Pierre Lindenbaum]

I'm pretty sure your VCF contains chromosomes named 1, 2,3,4... while the fasta uses a chr prefix "chr1","chr2","chr3",...

[ja4123]

There is some quick way to change prefix in one of that two files?

[Pierre Lindenbaum]

VCF files: Change Chromosome Notation