IBDNe

Program: ibdne.23Apr20.ae9.jar
Author: Brian Browning
Email: browning@uw.edu

Contents

Introduction

The IBDNe program estimate ancestry-specific historical effective population size. The input is a list of ancestry-specific identity-by-descent (IBD) segments. You can detecting IBD segments with the hap-IBD program. Breaks and gaps in IBD segments can be removed with the merge-ibd-gaps utility program.

If you use the IBDNe program in a published analysis, please cite the program version and the following article:

S R Browning and B L Browning (2015). Accurate non-parametric estimation of recent effective population size from segments of identity by descent. The American Journal of Human Genetics 97(3):404-418. doi: doi:10.1016/j.ajhg.2015.07.012

If you estimate ancestry-specific effective population size, we recommend citing and carefully imitating the examples in the following article:

S R Browning, B L Browning, R A Durazo-Arvizu, M L Daviglus, N Schneiderman, R C Kaplan, C C Laurie (2018). Ancestry-specific recent effective population size in the Americas. PLOS Genetics 14(5):e1007385. doi: 10.1371/journal.pgen.1007385

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Running IBDNe

To run the IBDNe program, enter the following command at the command line prompt:

cat [ibd] | java -jar ibdne.jar [arguments]

where [ibd] is a white-space separated list of IBD files produced by the hap-IBD program, and [arguments] is a space-separated list of parameter=value arguments. There are only two required arguments (map and out), and only one recommended argument (nthreads). An example command line for a 12-core machine is:

cat *.ibd | java -jar ibdne23Apr20.ae9.jar map=grch37.map out=ne nthreads=12

The IBDNe program will automatically exclude IBD segments that are shorter than the mincm parameter, and IBD segments in genomic regions having an extreme number of IBD segments.

Required Parameters

map=[file]
The map argument specifies a PLINK-format genetic map file with centiMorgan (cM) units. HapMap GRCh36 and GRCh37 genetic maps in PLINK format can be downloaded from here.
out=[prefix]
The out argument specifies the output filename prefix. All output files will have names that begin with this prefix.

Optional Parameters

nthreads=[positive integer]
The nthreads argument specifies the number of computational threads to use. The default nthreads parameter is the number of CPU cores on the host machine.
filtersamples=[true/false]
The filtersamples argument determines whether IBD segments from avuncular and closer relationships will be excluded. If the population sample is not random, setting filtersamples=true can improve the accuracy of the estimated effective population size in recent generations (default: filtersamples=true).
npairs=[non-negative number]
The npairs argument specifies the number of unordered haplotype pairs that produce the observed IBD. If npairs=0 then the number of haplotype pairs will be set equal to 2N*(2N-2)/2, where N is the number of distinct sample identifiers in the input IBD file (default: npairs=0).
nits=[positive number]
The nits argument specifies the number of algorithm iterations to use when estimating effective population size (default: nits=1000).
nboots=[positive integer]
The nboots argument specifies the number of bootstrap samples to use when computing confidence intervals for the estimated effective population size (default: nboots=80).
mincm=[positive number]
The mincm argument specifies the minimum IBD segment length in centiMorgan units. Any input IBD segments that have length shorter than the minimum length are ignored. The minimum IBD segment length should be sufficiently large so that IBD segments exceeding the minimum length are detected with high power and low false discovery rate (default: mincm=2).
trimcm=[non-negative number]
The trimcm argument specifies the length in centiMorgan units that is trimmed from each end of each chromosome or genomic interval. This trimming is used to correctly account for IBD segments whose end-point is censored by the end of the chromosome or genomic interval (default: trimcm=0.2).
gmin=[1 or 2]
The gmin argument specifies the minimum number of generations before the present that will have their effective population size estimated (default: gmin=2).
gmax=[integer≥4]
The gmax argument specifies the maximum number of generations before the present that will have their effective population size estimated. The default gmax parameter is determined by the mincm parameter (default: gmax=(600/mincm)).
seed=[integer]
The seed argument specifies the seed for the random number generator (default: seed=-99999).

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Controlling running time

The default parameters values are selected to give high accuracy. With default parameters, expect the IBDNe run-time to be several hours. Much faster computation times may be obtained with no loss in accuracy by increasing the nthreads parameter. Alternatively, faster computation times may be obtained with some loss in accuracy by reducing the nits or nboots parameters.

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Output files

Five output files are produced. Each output filename begins with the prefix specified with the out parameter and has a unique extension.

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Download IBDNe

The IBDNe program is licensed under the Apache License, Version 2.0 (the License). You may not use the IBDNe program except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.

The IBDNe program is distributed on an "AS IS" BASIS WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

ibdne.23Apr20.ae9.jar java executable file
ibdne.23Apr20.ae9.src.zip source code
ibdne_release_notes description of changes in recent versions

The following resources are also available:

hap-IBD a fast, haplotype-based IBD detection method
ASIBDNE tools and example scripts for ancestry-specific estimation of effective population size

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Copyright: 2016-2020 Brian L. Browning
Last updated: 23 April 2020