Question: Unable to find FASTA index entry for '1'
0
gravatar for ja4123
11 months ago by
ja41230
ja41230 wrote:

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?

freebayes bam vcf fasta • 516 views
ADD COMMENTlink modified 10 months ago • written 11 months ago by ja41230
2
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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

ADD COMMENTlink written 11 months ago by Pierre Lindenbaum131k

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

ADD REPLYlink written 11 months ago by ja41230
2

VCF files: Change Chromosome Notation

ADD REPLYlink written 11 months ago by Pierre Lindenbaum131k
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