snappy-pipeline
0.5.0

Pipeline Users Docs

  • Quickstart
  • Installation
  • Usage
  • Overview

Somatic pipeline

  • Mapping and friends
  • Panel of normals
  • Somatic variation filtration
  • Somatic CNV calling
  • Export to cBioPortal

Pipeline Step Docs

  • Pipeline Step Introduction
  • Generic Pipeline Step Description
  • Adapter Trimming
  • Germline Build Target Sequence gCNV Model
  • Germline Build WGS gCNV Model
  • HLA Typing
  • IGV Session Generation
  • NGS Data QC
  • NGS Mapping
  • Somatic Gene Fusion Calling
  • Somatic Purity & Ploidy Estimate
  • Somatic Targeted Seq. CNV Calling
  • Somatic Variant Annotation
  • Somatic Variant Calling
  • Somatic Variant Filtration
  • Somatic WGS CNV Calling
  • Somatic WGS SV Calling
  • Germline Targeted Seq. CNV Calling
  • Germline Targeted Seq. MEI Calling
  • Germline Repeat Expansion Analysis
  • Germline Variant Annotation
  • Germline Variant Calling
  • Germline Variant Sanity Checking
  • Germline Variant De Novo Filtration
  • Germline Variant Phasing
  • Germline Variant Filtration
  • Germline SV Calling
  • Germline WGS SV Filtration

Pipeline Developers Docs

  • Developer’s Introduction
  • Somatic Variant Calling Dissection
  • NGS Mapping Dissection
  • API Documentation

Project Info

  • Contributing
  • How To: Release
  • Credits
  • Changelog
  • License
snappy-pipeline
  • Search

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