Feature/range based normal panel

cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

http://cancerit.github.io/cgpPindel/

GNU Affero General Public License v3.0

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Closed keiranmraine closed 2 years ago

keiranmraine commented 2 years ago

This PR introduces the following:

Ability to run pindel.pl without flagging
- caveman has had this for a long time
- useful for building normal panels and other purposes
Introduces FF021
- alternate normal panel flag
- uses range-start & range-end positions of events
- split by event type D/I/DI for better accuracy
- Prevents large events being masked by small items
Updates pindel_np_from_vcf.pl
- Option added to switch generation mode to range based

keiranmraine commented 2 years ago

@AndyMenzies can you review the perl stuff? New flag and method for generating reference file.

Added nextflow binding for the NP generation (old and new supported) and pindel.pl. Additional docs on internal confluence to aid internal use.

Don't see a reason to not have this incorporated into a release as it's only active if you specify the new flag (do as pre-release).

AndyMenzies commented 2 years ago

Perl reviewed, looks good.