How to fix FreeBayes error "unable to find FASTA index entry for bed files"
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14 months ago
wlei091226 • 0

I'm trying to use freebayes to call variants through the following parameters using RNA-Seq data:

$freebayes --fasta-reference $ref \
--region $BED \
$bam \
> ${outdir}/${sample}.freebayes.vcf
and my bed files like this:
chr1:11868-12227
chr1:12612-12721
chr1:12974-13052
chr1:13220-14501
chr1:15004-15038
.....

but report an error:

unable to find FASTA index entry for '/path/to/GRCh38.exon.bed'

I'm pretty sure my fasta files have the index with the suffix .fai

Why did this happen?

freebayes variant-calling RNA-Seq • 674 views
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Entering edit mode

I have the same issue. I check correspondence between fasta headers line and bed column. Both have chr1 as "prefix". May that fasta file has, other than Chr1 to Chr22, ChrM, Unknwon and HLA--### contigs while bed file not?

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