Split up a Bam file with chrom-bed

[dmacmillan]

I saw a couple posts, not specifically here but elsewhere that asked how one could divide a "bam" file into certain chunks or into its individual chromosomes. Well while working with readDepth I wrote a python script that does this automatically. It can take a "bam" file and divide it into each chromosome, outputting to either bam or bed format. This is a big time saver if you are using the readDepth package. I figured I might as well share since it would be annoying to have to do this for every genome.

Yes its a basic command, yes it can easily be done with bash. I wanted to make the user interface command-line easy to follow, with additional help and usage features.

You can get the script here:
http://code.google.com/p/chrom-bed/

[gringer]

You can get the script here:

http://code.google.com/p/chrom-bed/

Note that this (currently) only works with human genomes (if I'm reading the code correctly). It would not work so well for transcriptomes, which have arbitrary transcript names that can't be predicted at the time of writing the code. While it would be possible to make it more generic, bear in mind that you'll be treading in territory that is within the realm of what pysam and HTSeq (which uses pysam for SAM file processing) are capable of:

http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/api.html

http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html#calculating-coverage-vectors

[dmacmillan]

It was designed for the human genome yes.