I am running Pindel against 30x coverage whole exome data then using the conversion utility to create vcf files from the Pindel outputs. I get a number of results. I can correlate the _D, _INV, _SI, _TD files with deletions,inversions, short insertions and tandem duplicates. I do not have _BP, _LI or _CloseEnd results that I might expect - well maybe my data, no problem.
However I do have _Int, _IntFinal and _Rp results....though my vcf files are header only, no vcf lines.
What is the meaning of the _Int, _IntFinal and _RP files?
Which SVs do they represent?
Why do I get a vcf file with just a header? I would expect that if I don't get a result file for Bps (breakpoints) because none are found in my data, then the same should be true for "RP" whatever that is.
Thank-you for your help.