Dragen variant calling

[j0ntt]

Hi,

While Dragmap is freely available, is the rest of the Dragen software also? Is it possible to download the software that performs the variant calling?

[ghost]

You can use gatk4 in dragen-mode for variant calling.

[j0ntt]

@zimmermf

Thank you. And is this Dragen mode somehow different from normal Dragen variant calling method?

[ghost]

Regarding your question, you can read this article on functional equivalence of both methods:
https://gatk.broadinstitute.org/hc/en-us/articles/4410456501915-Functional-equivalence-in-DRAGEN-GATK

I personally compared the GATK best-practices pipeline with DRAGEN-GATK using a mock-dataset and the DRAGEN pipeline had the same recall but a lower precision.
In my case, I had a substantially lower number of duplicates after duplicate marking when I used DRAGMAP for the alignment and haven't figured out yet why this is the case.