I have created .bam files using BWA and Samtools having downloaded a reference genome hg19 from UCSC and indexing it with
bwa index -a bwtsw hg19.fa
This worked fine for me, until now when I am trying to call variants in GATK and see that I need a reference in karyotypic order. I have downloaded the hg19.fa.fai and .dict files from the GATK FTP site and have also downloaded their full reference genome which is in chromosome order. I read that it wad easier to do this than to try and order the indexed reference I already have.
Only I am now trying to index the new reference in the same way and get the message:
[bwa_index] fail to open file '‐a bwtsw' : No such file or directory
Any ideas what I should be doing?!