Welcome to the Documentation of hapROH and hapCon

Contents:

• Overview
  • Citing
  • Contact
  • Acknowledgments
• Installation
  • Upgrading
  • c Extension
  • Dependencies
• hapROH
  • Scope of the Method
  • Getting started
  • Download reference Data
  • Example Use Case: Vignettes
  • Development
• hapCon
  • Application range of hapCon
  • Input
  • Getting started
  • Example Use Case: Vignettes
• hapCon_ROH
  • Introduction
  • Input
  • Usage
  • Scope of this method
  • Example Usage 1: Identify ROH blocks for contaminated samples
  • Example Usage 2: Identify false positive ROH blocks
• Frequently Asked Questions (FAQ)
  • I have a .bam, what should I do?
  • With the roh.csv and roh_full.csv tables, what is the difference between the length/lengthM, start/startM and end/endM columns?
  • Why is the value of lengthM sometimes multiplied per 100?
  • How can I implement hapROH for another set of SNPs, such as all 1000Genome SNPs?
• API Reference
  • hapsburg

Indices and tables

• Index

• Module Index

• Search Page