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
Workflow | Genotype Calls VCF | Final VCF | SNPs | INDELs |
|---|---|---|---|---|
Iliad’s Raw Sequence Module | – | 119,960,362 | 9,520,169 | 498,893 |
OVarFlow | 610,405,020 | 4,034,429 | 3,623,864 | 411,214 |