How could I compare variant calling results?

Hello, I saw a post on your homepage that the results of the HaplotypeCaller of Parabricks are the same as those of GATK4 HaplotypeCaller.
Does this really have 100% matching results?

How did you compare the results? I compared the results of the VCF file for both of Parabricks and GATK4 using Illumina/hap.py, but the results were not the same. I’d like to know how you compared the variant calling results.

I look forward to your answer.

Thank you.

Hey @qhtjrmin,

Here is the page where we discuss how to compare the outputs of Parabricks vs GATK:

The results will depend on which versions of Parabricks and GATK you are comparing. Parabricks Version 2 will align with GATK 4.0.4 and Parabricks Version 3 will align with GATK 4.1