Need help understanding Pindel outputs
0
6
Entering edit mode
6.8 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 • 2.9k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 3184 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6