IBD based recombination estimation (IBDrecomb) is an efficient method for constructing fine-scale genome-wide recombination maps. It can be applied to IBD segments inferred from population-based samples with thousands of individuals. IBD segments may be inferred using Refined IBD (http://faculty.washington.edu/browning/refined-ibd.html).
Zhou Y, Browning BL, Browning SR. Population-specific recombination maps from segments of identity by descent. The American Journal of Human Genetics. 2020 Jul 2;107(1):137-48.
To install IBDrecomb in a linux environment, download the source files and decompress them if necessary, then go to the directory 'src/' and type
make
the executable file IBDrecomb can be used to estimate recombination rates based on the input IBD segments and customized parameters. For example, you can go to the example directory and run test as
cd ../example/
../src/IBDrecomb -refinedibd test.1.ibd.gz -fbin 10000 > test.10000.map
The IBD input can be a plain text file or a gzip-compressed file (.gz), which can be in refined-IBD's format ('-refinedibd') or a generic format ('-ibd') that each line recording the starting position and ending position of an IBD segment. In this example, the parameter '-fbin 10000' specifies the estimation at scale 10kb and the output is saved to the file 'test.10000.map'. In reality, the estimation interval might be a slight smaller than the customized size because the whole estimation region length (in bp) is not capable of being divided by the interval size without a remainder. The default output map is in plink map format, which includes four columns: chromosome name, variant identifier (set as '.'), genetic position, and physical coordinate.
Recombination rates and genetic positions are normalized by the parameter '-rate', which is the average recombination rate over the estimation region. The value of the rate parameter should be obtained from a family-based reference map. If the average rate is 1.21cM/Mb, then we can run the program as
../src/IBDrecomb -refinedibd test.1.ibd.gz -fbin 10000 -rate 1.21 > test.10000.normalized.map
Users can also customize advanced parameters such as the bin size. A full list of parameters and their default values can be found by typing
../src/IBDrecomb -help
Usage: IBDrecomb [options] parameters
(Required inputs:)
-refinedibd/-ibd <filename> # IBD segments input, '-refinedibd' for the refined-IBD's output format and '-ibd' for the two-column generic format
-fbin <integer> # Bin size(bp) for outputing recombination rates
(Optional parameters:)
-bin 500000 # Bin size(bp) for first step of estimation
-rate 1.0 # Average cM/Mb to normalize the estimated recombination rates
-trim 1 # Length(bp) to trim at chromosome ends
-fold 1 # Relative size of adjunct-region to the end-region (see Methods of the published paper)
-iter 20 # Number of iterations
-chr . # Chromosome to estimate
-help # Print this help file
This program 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.
This program 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 should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
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