SAMtools-1.2 sort options documentation

Question

[deanpett]

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.

Answer 1

[John Marshall]

If when you type samtools sort, the usage display you get is

Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>

then the samtools that you are actually running is 0.1.18. (When you just type samtools and get a list of subcommands, what version number does it report above the list of subcommands?)

You should check your $PATH etc, because it would appear you are not running the samtools executable that you think you are.