Refined IBD

Program: refined-ibd.12Jul18.a0b.jar
Author: Brian Browning
Email: browning@uw.edu

Contents


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.12Jul18.a0b.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.12Jul18.a0b.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.

refined-ibd.12Jul18.a0b.jar Refined IBD program
refined-ibd.23Dec17.pdf Refined IBD documentation
run.refined-ibd.12Jul18.a0b a unix script which runs a test Refined IBD analysis

The following resources are also available:

refined-ibd.12Jul18.a0b.zip Refined IBD source code
human genetic maps HapMap GrCh36 and 37 genetic maps in PLINK format with cM units
relatedness_v1.py A python program for estimating relatedness from IBD segments
utilities a suite of utility programs
Beagle the Beagle web page
Variant Call Format an introduction to Variant Call Format (VCF)

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Copyright: 2013-2018 Brian L. Browning
Last updated: 17 September 2018