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?!
What version of bwa and what is the exact command that causes the error message?
Hi it is bwa-0.7.12 and the command was
Are you sure you didn't type:
or something like that? This isn't an error that I can reproduce without using an incorrect command.
100% sure, I used the same command I have used in the past so I don't know why it wont work. In the BWA directory I see bwtsw files with various suffixes. At the moment I am running index alone (without bwtsw) but I am not familiar with how this works for the human genome.
Oh ok brilliant, thank you. The index command alone is processing nicely so I wont question it any more!