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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Pindel Output files #40

Open ghost opened 8 years ago

ghost commented 8 years ago

Hi, I have two output files ending in '_INT_final' and '_CloseEndMapped' which I cannot seem to find any information about. What are these files and what should they contain (both are empty)?

Thanks

angadps commented 8 years ago

This might be a little late but still...

The CloseEndMapped file should contain information on reads for which only one end could be mapped. This corresponds to the -s option when calling pindel which is turned off by default. That's why it may be empty. -s/--report_close_mapped_reads report reads of which only one end (the one closest to the mapped read of the paired-end read) could be mapped. (default false)

The _INT_final I suppose contains interchromosomal event information.