Question

Samtools Depth Can Only Have Stdout?

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11.9 years ago

Chris ▴ 40

Hi, everyone! I want to have a look at the depth of each position in my .bam file, so, the samtools used,samtools depth my.bam, but I find I can't get the output parameter, it only output in my Terminal screen. I want a file with whole positions' depth. How can I do it? Thx!

samtools depth-of-coverage output • 5.6k views

ADD COMMENT • link updated 11.9 years ago by Pierre Lindenbaum 161k • written 11.9 years ago by Chris ▴ 40

score 2 · Answer 1 · 2012-06-14

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11.9 years ago

Leszek 4.2k

In unix you can redirect stdout to file:

samtools mpileup bam > out.txt

ADD COMMENT • link 11.9 years ago by Leszek 4.2k

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Thx a lot. So simple, I am really a Novice!!

ADD REPLY • link 11.9 years ago by Chris ▴ 40

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if you like the answer, accept it with a tick.

ADD REPLY • link 11.9 years ago by Leszek 4.2k

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Does mpileup and depth have any difference?

ADD REPLY • link 11.5 years ago by camelbbs ▴ 710

score 1 · Answer 2 · 2012-06-14

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11.9 years ago

Leonor Palmeira 3.9k

I suppose you just want to redirect the output of your command into a file. This is not a bioinformatics question, but a UNIX question.

Anyway, you should use the redirection character (>) and your syntax should look like:

samtools_command -andoptions inputfile > outputfile

ADD COMMENT • link 11.9 years ago by Leonor Palmeira 3.9k

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Thanks a lot!!!!

ADD REPLY • link 11.9 years ago by Chris ▴ 40

score 1 · Answer 3 · 2012-06-14

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11.9 years ago

Pierre Lindenbaum 161k

try to use the pipeline redirection: http://www.codecoffee.com/tipsforlinux/articles2/042.html

samtools depth file.bam > result.txt