Question: difference between DRAGEN and GATK
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gravatar for Sara
4 weeks ago by
Sara90
Sara90 wrote:

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?

genome • 98 views
ADD COMMENTlink written 4 weeks ago by Sara90

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?

ADD REPLYlink written 4 weeks ago by genomax87k

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

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by German.M.Demidov1.8k
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