I'm trying to use freebayes but I keep running into this problem. Does anyone know who to fix this? I was looking at this tutorial for commands but it doesn't seem to work. I can seem to get it to recognize my fasta file or my .bam file. I don't know if I did something wrong or what.
./freebayes -f felCat8.fa --region E2:1-100000 \ test.bam >test.vcf
index file felCat8.fa.fai not found, generating...
ERROR(freebayes): Could not open input BAM files
BamMultiReader::Open: unable to open all files:
unable to open file: test.bam
I have also tried and got the same error
./freebayes -f felCat8.fa -b test.bam >test.vcf