Refined IBD

Contents

• Introduction
• New features
• Removing breaks and gaps in IBD segments
• Download

Introduction

Refined IBD is a software package that detects identity-by-descent segments in phased genotype data. If you use Refined IBD in a published analysis, please report the program version and cite:

B L Browning and S R Browning (2013). Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194(2):459-71. doi:10.1534/genetics.113.150029

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New features

This version of Refined IBD is a stand-alone program with four improvements to the version of Refined IBD in Beagle 4.1:

1. Parameters have been simplified.
2. All length parameter parameters (e.g. window, ibd, and trim) are in cM units.
3. The overlap between adjacent sliding windows is set automatically.
4. The .ibd and .hbd output files have an additional column containing IBD segment lengths.

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Removing breaks and gaps in IBD segments

Haplotype phase errors and genotype errors can cause breaks and gaps in the detected IBD segments. You can use the merge-ibd-segments.17Jan20.102.jar program to remove any breaks and short gaps in IBD segments. We usually remove gaps between IBD segments that have at most one discordant homozygote and that are less than 0.6 cM in length.

Enter "java -jar merge-ibd-segments.17Jan20.102.jar" for usage instructions.

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Download

Refined IBD is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Refined IBD is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You can download a copy of the the GNU General Public License from http://www.gnu.org/licenses/.

Source files in the net/sf/samtools/ directory are from the Broad Institute and are licensed under the MIT License. The net/sf/samtools/ files are used to perform BGZIP decompression.

The following resources are also available:

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Copyright: 2013-2020 Brian L. Browning
Last updated: 17 Jan 2020