Table 1.
Software requirements and availability.
Fig 1.
The GermVarX workflow comprises two primary phases: per-sample processing and cohort-level processing and annotation.
Fig 2.
GermVarX variant benchmarking.
Benchmarking of GATK-Join, DV-GLN, and Consensus strategies for SNPs and INDELs. DV-GLN and Consensus show highest SNP accuracy, while GATK-Join provides balanced INDEL performance.
Table 2.
Resource usage across GermVarX pipeline stages. The complete pipeline finished in 77.8 hours of wall-clock time. Reported CPU and wall-clock hours are cumulative task sums across all samples in each stage, not actual elapsed runtime.
Table 3.
Comparison of GermVarX with existing WES workflows.