Question: What is the "-" option of samtools?
0
gravatar for vw
5 weeks ago by
vw20
vw20 wrote:

Hi all,

I saw a command line:

samtools view -u alignment.sam | samtools sort -@ 4 - output_prefix

from samtools (conversion from .sam to .bam) and sorting of .bam file

I don't know the function of the - before the output_prefix. I cannot find it in the manual book.

Could you help me figure out it?

Thank you!

samtools • 141 views
ADD COMMENTlink modified 5 weeks ago by Pierre Lindenbaum121k • written 5 weeks ago by vw20
2
gravatar for Pierre Lindenbaum
5 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

'-' just means stdin/standard input

http://www.htslib.org/doc/samtools-1.2.html

Samtools is designed to work on a stream. It regards an input file - as the standard input (stdin) and an output file - as the standard output (stdout).

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Pierre Lindenbaum121k

Thank you! You solved my question.

ADD REPLYlink written 5 weeks ago by vw20
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