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I have this line

samtools view -h file | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o output

the dash between the -S and the -b is supposed to indicate to the program that it is from STDIN. I can run it from a perl script on the command line but as soon as I try to move it into a shell script it just creates the file without outputting any data. Any ideas would be greatly appreciated.

Dijkgraaf
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user1234579
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2 Answers2

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If you haven't already, have a look at the samtools FAQ. This has examples for doing similar things to what you want to do with your pipeline.

Its been a while since I used samtools, but I would've written your command like this:

samtools view -h file | awk '$3=="chr$a" || /^@/' | samtools view -S -b - > output.bam

Also you mentioned you had moved the command to a shell script. Is the shell script doing anything else? If it still doesn't work, I would post that for us to look at.

MattLBeck
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  • the shell script for a in {1..22} do samtools view -h AD3.sorted.bam | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o chr$a.bam done – user1234579 Mar 02 '12 at 14:36
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In a shell script the $a inside single quotes will not be expanded:

for a in {1..22} do 
  samtools view -h AD3.sorted.bam | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o chr$a.bam 
done
stark
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