difference between DRAGEN and GATK

Question

[Sara]

I have WES data and tried to make VCF file using GATK4 and DRAGEN but got different results. for both tools I used default setting and for both I did not target (bed) file. do you have any idea what the reason of this difference could be?

[GenoMax]

Start by looking at the versions of GATK. There are substantial differences between newer GATK v.4.1.x and older versions. Are you using DRAGEN's implementation of GATK to do the end-to-end analysis? Did you use the latest GATK for manual analysis?

[German.M.Demidov]

I think (if I recall correctly) Dragen started with GATK as a variant caller, but re-wrote it in the end to improve the performance. So maybe the key of the difference is that different algorithms were used.

https://gatk.broadinstitute.org/hc/en-us/articles/360039984151-DRAGEN-GATK-Update-Let-s-get-more-specific