Question: Unable to find FASTA index entry for '1'
0
gravatar for ja4123
5 weeks 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 • 124 views
ADD COMMENTlink modified 7 days ago • written 5 weeks ago by ja41230
2
gravatar for Pierre Lindenbaum
5 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k 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 5 weeks ago by Pierre Lindenbaum125k

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

ADD REPLYlink written 5 weeks ago by ja41230
2

VCF files: Change Chromosome Notation

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum125k
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