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moiexpositoalonsolab / grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
http://grene-net.org
GNU General Public License v3.0
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GATK Realigner #2

Closed florianhahn87 closed 3 years ago

florianhahn87 commented 3 years ago

Hey again :)

Is it possible to add the RealignerTargetCreator and the IndelRealigner from GATK to the pipeline as this always improves our alignments a lot or am I missing an option in the config.yaml file where I can do that already?

Thanks a lot, Florian

lczech commented 3 years ago

Hey Florian,

it seems that GATK4 HaplotypeCaller (which we use here) already does these steps, making the GATK3 tools you mentioned obsolete. See the end of this post:

Yes we dropped the indel realignment step from the Best Practices; I think that was about 2 years ago. There was a blog post about it. We found that this step was no longer useful when the variant calling was done with HaplotypeCaller or Mutect2, which implement a more sophisticated and effective form of realignment.

I couldn't find this blog post, but still, it seems, support for these tools has been dropped. So, I guess you should be good without them - what do you think? Furthermore, the RealignerTargetCreator seems to create an "intervals" file as its output, and I am not sure how this would help or be incorporated into the downstream steps.

Cheers Lucas

florianhahn87 commented 3 years ago

Oh, perfect, thanks for the clarification, we missed that change from GATK3 to 4! Thanks!