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/
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/
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