Interpreting Pindel _INT output format

[Jonathan Ellis]

I've run Pindel with the --report_interchromosomal_events flag, and on completion I have two files ending in _INT and _INT_final which I'm assuming contain the interchromosomal events. However, I can't find any documentation on the format of these files.

At first glance the format seems simple enough to understand, but in the _INT_final file, I'm seeing multiple events with the exact same breakpoints (I've attached a sample output file), and some of them have very similar breakpoints. This makes me think there are some subtleties in the format I'm not appreciating.

Does any body know what the difference between the two files is, and can any one help me with the interpretation of the output?

Thanks.

[KaiYe]

The one with final is a summary and should have a higher specificity. sorry for not documenting it. The file format is not final and we eventually will convert it to vcf.