samtools sort: legacy usage

Question

[c.e.chong]

Hi,

I am trying to run the command samtools sort -@ 12 in.bam -O bam in_sorted using samtools version 1.1.

However this gives me the error:

Legacy usage: samtools sort [options...] <in.bam> <out.prefix>
Options: 

  -f         Use <out.prefix> as full final filename rather than prefix
  -o         Write final output to stdout rather than <out.prefix>.bam
  -l,m,n,@   Similar to corresponding options above

Usage: samtools sort [options...] [in.bam]

Options:

  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -O FORMAT  Write output as FORMAT ('sam'/'bam'/'cram')   (either -O or
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam       -T is required)
  -@ INT     Set number of sorting and compression threads [1]

Should I not use -O and -@ with this version of samtools to specify that I want to use 12 threads and my output to be a bam file?

Thank you in advance for your help!

[WouterDeCoster]

Is there a good-enough reason to do this? Shouldn't you rather use the most up to date version and that syntax?

[c.e.chong]

I am trying to use the most up to date version of the syntax. My understanding was that the options -@ and -O are the new versions, not the legacy version?

[WouterDeCoster]

I don't know when -@ was introduced, but you no longer need -O. samtools finds the file format based on the extension specified by -o.

So you can do samtools sort -@12 -o sorted_alignment.bam myalignment.bam

[c.e.chong]

I tried this and it worked. Thank you for your help!!

Answer 1

[h.mon]

edit:

As you are using SAMtools 1.1, you should use the "current" command line, not the "legacy":

samtools sort -@ 12 -o in_sort.bam in.bam

end of edit:

If you want to follow the "legacy" usage, you can't put an option between in.bam and out.prefix, so your command line should be:

samtools sort -@ 12 -O bam in.bam in_sorted

[c.e.chong]

Hi,

Thank you for your help!

I tried this, but I still got the same error?

I assumed I was not using the "legacy usage" as both -@ and -O are included in the given options of the new version?

[h.mon]

Try:

samtools sort -@ 12 -o in_sort.bam in.bam

[c.e.chong]

I tried this and it worked. Thank you for your help!!

[WouterDeCoster]

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