Has anyone else noticed issues regarding the options of the SAMtools "sort" function?
I've been trying to use a couple of extra cores of my server to speed up the process but the -@
option is not recognized. While the documentation lists many options:
samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] -T *out.prefix [-@ threads] [in.bam*]
I'm only able to use those described by the function itself when I try to run it in the command line, which differs in the order of inputs as well:
Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>
Any ideas? Updated documentation needed over at samtools? am I missing something (I'm using samtools-1.2, which I believe should match the published documentation)?
Thanks in advance.