Table 2 Comparison of genotype and variant data type between Iliad and OvarFlow calculated with BCFtools ‘stats’ flag. The ‘Genotype Calls VCF’ represents the count of records in Step “06_combined_calls” within OVarFlow. The ‘Final VCF’ (records) generated from OVarFlow’s pipeline is the reduced variant-only file. Iliad produces a singular final VCF within its pipeline that calls a specific set of annotated genomic positions from NYGC [30]. A breakdown of the number of SNPs and INDELs within the VCF is reflective of the pipelines’ respective variant callers