Need help understanding Pindel outputs
Entering edit mode
7.5 years ago
nr6001998 ▴ 60

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.

Pindel • 3.0k views
Entering edit mode

Having the same issue 2.7 years later! Did you find out? Can you comment?


Login before adding your answer.

Traffic: 1624 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6