samtools and I/O redirection

Question

[wangdp123]

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

[Gabriel R.]

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

Answer 1

[WouterDeCoster]

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