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?