We have 2 vcf (Whole Exome Sequencing (WES) data; germline samples) files (e.g., vcf_1 and vcf_2). vcf_1 was generated (Ref. genome: hg38) using the GATK pipeline for 250 children and their parents and vcf_2 was generated (Ref. genome: hg38) using the DRAGEN pipeline for another 50 children and their parents (Samples are different). These are raw vcf files and I have not applied any quality-related false positive filters to them.
Now, when we compare the sample-wise SNV counts from vcf_1 and vcf_2, there is a huge difference. vcf_2 contains on average 4-6 times lesser number of SNVs per sample than vcf_1.
N.B: I found this article (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418901/), where it has been reported that the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample was around 98k, respectively, for WES. For our case, in the case of GATK-generated vcf samples, this varies from 130k to 188k, and for DRAGEN-generated vcf samples, this varies from 30k to 40k.
I understand both pipelines (GATK and DRAGEN) implement different methods to generate vcf files but is it common/normal to examine that much difference in SNV counts? I would appreciate it if someone can give some explanation (or provide some materials) about it.