index.md

GSvar documentation

NOTE: This documentation is work in progress. Please contact Marc Sturm if you have suggestions for additional content!

Basics

• Data analysis (pipelines, status, restarting...)

Variant filtering and QC

Germline analysis:

• Sample quality control
• Small variant analysis
• CNV analysis
• SV analysis
• Repeat expansions analysis
• ROH analysis
• Report generation

Other analysis

• RNA analysis

Auxilary functionality

• IGV integration
• Preferred transcripts
• Variant publication
• Burden test

Misc

• Configuration
• ChangeLog
• FAQ