I'd like to combine my paired-end reads that have already been mapped by a PE reference aligner. Is there an existing tool for stitching overlapping, mapped paired-end reads (presumably from SAM to SAM)?
I've taken a look at COPE, PEAR, and FLASH, but it seems that none of these will merge a SAM/BAM. I'm looking at ABySS right now, but I'm not confident that any of these are built for merging non-FASTQ input.
It seems like my only options are either to 1.) stitch my FASTQ pairs prior to mapping or 2.) parse the SAM fields to do the stitching myself. I'd like to work with a validated alignment pipeline, so I'd rather not switch the pipeline from paired-end to single, stitched reads.