Skip to content

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

License

Notifications You must be signed in to change notification settings

CERC-Genomic-Medicine/WEGS_pipelines

Repository files navigation

Variant calling pipelines

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).

About

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Contributors 4

  •  
  •  
  •  
  •