Help with samtools command

Question

[Mehmet]

Hello All,

Can anyone give me a detailed explanation about this command?

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

I had read some tutorials, but I didn't understand how to use the parameters.

Thanks

Answer 1

[GouthamAtla]

This is a basic linux command syntax

The ones in [ ] are optional and the ones in < > are necessary arguments.

SO samtools sort command takes two mandatory options, one is input.bam and output_bam_prefix. The -n -o and -m are optional.

[Devon Ryan]

Moving this to an answer. It's detailed enough IMO.