SNAPPY Pipeline

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Pipeline Users Docs

Quickstart
Installation
Usage
Overview

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
NGS Sanity Checking
Somatic Gene Fusion Calling
Somatic Neoepitope Prediction
Somatic NGS Sanity Checking
Somatic Purity & Ploidy Estimate
Somatic Targeted Seq. CNV Calling
Somatic Variant Annotation
Somatic Variant Calling
Somatic Variant Checking
Somatic Variant Expression
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
T cell CRG Report
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

Germline SV Calling
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Germline SV Calling

Implementation of the sv_calling_wgs step

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© Copyright 2015-2021, CUBI, Berlin Institute of Health. Revision 46b2303d. Last updated on Sep 20, 2023.

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