What is does

BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).

DANGER: Multiple Outputs

As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing.

How it works

The following options can be specified via "Split BAM dataset(s) by" dropdown:

Mapping status (-mapped)          split mapped/unmapped and generate two output files
                                  named (MAPPED) and (UNMAPPED) containing mapped and unmapped
                                  reads, respectively.

Pairing status (-paired)          split single-end/paired-end alignments and generate two output files
                                  named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
                                  reads, respectively.

Reference name (-reference)       split alignments by reference name. In cases of unfinished genomes with
                                  very large number of reference sequences (scaffolds) it can generate
                                  thousands (if not millions) of output datasets.

Specific tag (-tag)               split alignments based on all values of TAG encountered. Choosing this
                                  option from the menu will allow you to enter the tag name. As was the
                                  case with the reference splitting above, this option can produce very
                                  large number of outputs if a tag has a large number of unique values.

More information

Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki