I have a sorted and indexed .bam file, and I am running it through freebayes, with the script : "freebayes -f /path/to/reference.fasta Bamfile.bam > NewVCF_file.vcf" I have in the directory I am running this script from, and in the directory that the reference file is in the index files for the reference, the .fai and .dict files. Every time I run this script I get the "Unable to find FASTA index entry for 'unitig_2993_pilon error. " Even know I have the index files.
I have gone back and used Picard tools to remake the .dict file and used the samtools faidx command to make the .fai reference file.
Is there something I'm not doing? I have the correct Bam file and index files and it just continually throws the indexing error. What could be the problem here?