This repository includes Nextflow pipelines for variant calling from WES, WGS, and WEGS data.
- JointVariantCalling - this directory contains pipelines for joint genotyping in large cohorts.
- VariantCalling - this directory contains pipelines for single sample genotyping in small cohorts.
- WES+WGS - this directory contains pipelines for merging reads from WES and WGS to produce WEGS (Whole Exome/Genome Sequencing) data.
- BenchmarkVariants - this directory containts pipeline for benchmarking genotyping accuracy.
- StructuralVariantCalling - this directory containts pipeline for calling SVs (Structural Variants).