GATK Realigner about grenepipe HOT 2 CLOSED

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

from grenepipe.

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

from grenepipe.