Tool which splits bam files into specific genomic intervals?

[Alex Coventry]

I think I see how to use bamtools to split bam files into individual chromosomes. Is there a tool which will take a list of subchromosomal genomic intervals, and split the reads in a bam file by those intervals? I know how to do this with samtools, but having to resort and reindex each of the resulting bamfiles is slow...

[swbarnes2]

BEDTools can take a .bed file and a .bam file and return a .bam file consisting of reads that intersect the regions in the .bed file.

So you'd probably have to run BEDTools once for every region, but you don't have to index the .bam file.

[maubp]

Has anyone done the reverse?

I am thinking of a SAM/BAM file for FASTA set of contigs, plus and a FASTA set of scaffolded supercontigs consisting of the contigs joined with runs of NNNNN (perhaps in some cases with a contig reverse complemented). I would like to be able to produce a new SAM/BAM file against the scaffolded supercontigs - where rather than remapping the reads, the existing mapping is reused by editing the reference names and offsets (with more care needed when a contig has been reverse complemented). Clearly it isn't quite as straightforward as that once you have paired end data, since when read pairs mapped to two different contigs are now placed on the same supercontig, you may want to update their FLAG to say they are now properly mapped.