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samtools and I/O redirection

Hello,

I am using 2> and 1> to output the stderr and stdout to two files but when I use samtools to convert test.bam into test.sam, it seems that there is no output in the result file (test.sam).

samtools view -h test.bam > test.sam 2> bam2sam.stderr 1> bam2sam.stdout

Would you like to help me out?

Many thanks,

Tom

samtools
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written by wangdp123 wangdp123

let's take a step back, why do you want a sam file to begin with?

• 1 views • link
written by Gabriel R. Gabriel R.

1 answer

you use samtools to write to stdout to test.sam, but then you redirect stdout to another file. Not surprisingly, test.sam remains empty...

• 1 views • link
written by WouterDeCoster WouterDeCoster

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