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Is it possible to output bwa output directly into samtools view to convert into bam format without using intermediate files? I am running low on hard disk space and I am attempting to automate my script. I would like to convert my bwa output to bam, sort it, and index it. I know the sam-bam conversion can be piped into the sort command, but is it possible for the samtools view to take its input from STDIN?
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figured out on linux at least, if I give it the filename /dev/stdin that will satisfy it since the OS does the work, even though samtools does not appear to be expressly programmed to switch to stdin.
It appears to be working too, which is going to save me some headaches.
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apparently I could also have done this with named pipesLast edited by Kotoro; 07-18-2011, 04:06 PM. -
bwa + samtools have been developed with pipes in mind:Originally posted by Kotoro View Post
HTHCode:$ bwa aln [OPTIONS] [DB] [FASTQ] | bwa samse [OPTIONS] [DB] - [FASTQ] | samtools view -Su - | samtools sort - [PREFIX]
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Almost, this should work (essentially it is a double process substitution).Originally posted by gavin.oliver View Post
Code:$ bwa sampe [OPTIONS] [DB] <(bwa aln [OPTIONS] [DB] [FASTQ1]) <(bwa aln [OPTIONS] [DB] [FASTQ2]) [FASTQ1] [FASTQ2] | samtools view -Su - | samtools sort - [PREFIX]
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Thanks!
The wonders of the command line, eh?
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