Hi All,

I would like to ask that is there an accurate tool/script for deinterleaving fastq files? I managed a 'bam to fastq' conversion according to http://gatkforums.broadinstitute.org/discussion/2908/howto-revert-a-bam-file-to-fastq-format and I would like to deinterleave the output fastq.

Many thanks!
[Reformat][1] can do that, if you're sure the resulting fastq file is interleaved. You can run with the "vint" and "ain" flags to verify that it is interleaved properly. If it's not, you can fix it by running repair.sh (also in the BBMap package).

 [1]: http://seqanswers.com/forums/showthread.php?t=46174