How to fix FreeBayes error “unable to find FASTA index entry for bed files”

How to fix FreeBayes error “unable to find FASTA index entry for bed files”

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?


calling


freebayes


variant


RNA-Seq

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