Program: | ibdne.23Apr20.ae9.jar |

Author: | Brian Browning |

Email: | browning@uw.edu |

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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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.

**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.

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

- The
**.log**file contains the analysis parameters and a summary of the analysis. - The
**.pair.excl**file contains closely-related sample pairs whose IBD segments were excluded from the analysis. - The
**.region.excl**file contains genomic regions that were excluded from the analysis. Any genomic region that is less than 50 centiMorgans in length and bounded on each side by a chromosome boundary or a locus with an extreme number of IBD segments is excluded. - The
**.ne**file contains the estimated effective population size in each recent generation and its 95% bootstrap confidence interval. - The
**.boot**contains the estimated effective population size in each recent generation for the original data (line 1) and for each bootstrap sample (following lines). The*k*-th field of each line is the estimated effective population size*k-1*generations before the present.

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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