I have to use DRAGEN for small variant calling and generating VCF files. at this step I am doing benchmarking to see the results of that.
my colleague have done the same analysis using GATK3. then I compared the sites in my vcf file (made using DRAGEN) and the vcf file which was made using GATK and I realized there is almost 65% overlap between 2 vcf files and the others are unique for every file.
Since they have different algorithms (for both tools we used defaults settings), it is expected to have different results but in this case, the difference is a lot and we have a lot of missing variants when we discussed that with biologists.
so, the question is that do you have any idea how we can solve this issue in DRAGEN.
BTW, I run DRAGEN on the illumina's cloud (basespace).
You could try contacting Illumina tech support for DRAGEN.
There are differences in DRAGEN's GATK implementation (which you are using). These are supposed to be reconciled in a uniform release at some point this year. I don't believe that has happened yet.