This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Piped Commands, Picard to BWA

I'm new to NGS analysis and was wondering how to run a piped command to avoid reading and writing huge intermediate files. I only have a little experience with the linux commands, but I am running from inside a GATK docker image.

Does the command line just look like...

gatk RevertSam (stuff) -F /dev/stdout | bwa mem (stuff) /dev/stdin

Also, is using a piped command like this optimal for this situation? I've read that sometimes, since piped commands run concurrently, it doesn't provide much benefit with huge files

Any advice on this would be appreciated! Trying to learn more about NGS analysis and linux in general

bwa picard piped
• 788 views • link
written by aalith • aalith

Hello aalith!

We believe that this post does not fit the main topic of this site.

This is already under discussion. If picard does not work, use samtools, which works perfectly.

See Pipe SamToFastq, BWA mem not working

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by ATpoint ATpoint

Sorry if this doesn't fit into the site's focus. but the other thread hadn't answered why the piped command may not work. There's an error about not being able to write to dev/stdout for some reason. Is there any way around this besides using samtools?

• 0 views • link
written by aalith • aalith

We will not discuss that here. This is not meant to be impolite but aims to keep information on a single thread rather than splitting it over many. If it doesn't work and no one provides feedback yu'll have to live with it and try something else. samtools is a perfectly right alternative and by now the job would've by long been finished. Do not waste time on this lowlevel stuff, just use samtools and go on.

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this