Editing Identity by descent (section)

== Methods and software ==
Programs for the detection of IBD segments in unrelated individuals:
* [https://www.biorxiv.org/content/early/2017/01/26/103325 RAPID]: Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform <ref name="Naseri 2017">Naseri A, Liu X, Zhang S, Zhi D. Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform BioRxiv 2017.</ref>
* [http://parente.stanford.edu/ Parente]: identifies IBD segments between pairs of individuals in unphased genotype data<ref name="Rodriguez 2013">Rodriguez JM, Batzoglou S, Bercovici S. An accurate method for inferring relatedness in large datasets of unphased genotypes via an embedded likelihood-ratio test. RECOMB 2013, LNBI 7821:212-229.</ref>
* [http://faculty.washington.edu/browning/beagle/beagle.html BEAGLE/fastIBD]: finds segments of IBD between pairs of individuals in genome-wide [[Single-nucleotide polymorphism|SNP]] data<ref name="Browning.2011">{{Cite journal
| last1 = Browning | first1 = B. L.
| last2 = Browning | first2 = S. R.
| doi = 10.1016/j.ajhg.2011.01.010
| title = A Fast, Powerful Method for Detecting Identity by Descent
| journal = The American Journal of Human Genetics
| volume = 88
| issue = 2
| pages = 173–182
| year = 2011
| pmid = 21310274
| pmc =3035716
}}</ref>
* [https://web.archive.org/web/20131231192206/http://faculty.washington.edu/browning/beagle/b4.html BEAGLE/RefinedIBD]: finds IBD segments in pairs of individuals using a hashing method and evaluates their significance via a likelihood ratio<ref name="Browning.2013b">{{Cite journal
| last1 = Browning | first1 = B. L.
| last2 = Browning | first2 = S. R.
| doi = 10.1534/genetics.113.150029
| title = Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data
| journal = Genetics
| volume = 194
| issue = 2
| pages = 459–471
| year = 2013
| pmid = 23535385
| pmc =3664855
}}</ref>
* [http://faculty.washington.edu/browning/ibdseq.html IBDseq]: detects pairwise IBD segments in sequencing data<ref name="Browning.2013">{{Cite journal
| last1 = Browning | first1 = B. L.
| last2 = Browning | first2 = S. R.
| doi = 10.1016/j.ajhg.2013.09.014
| title = Detecting Identity by Descent and Estimating Genotype Error Rates in Sequence Data
| journal = The American Journal of Human Genetics
| volume = 93
| issue = 5
| pages = 840–851
| year = 2013
| pmid = 24207118
| pmc =3824133
}}</ref>
* [http://gusevlab.org/projects/germline/ GERMLINE]: discovers in linear-time IBD segments in pairs of individuals<ref name="Gusev.2009"/>
* [http://www1.cs.columbia.edu/~gusev/dash/ DASH]: builds upon pairwise IBD segments to infer clusters of individuals likely to be sharing a single haplotype<ref name="Gusev.2011"/>
* [https://web.archive.org/web/20131124040826/http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml PLINK]: is a tool set for [[whole genome association]] and population-based linkage analyses including a method for pairwise IBD segment detection<ref name="Purcell.2007"/>
* [http://www.popgen.dk/software/index.php/Relate Relate]: estimates the probability of IBD between pairs of individuals at a specific locus using SNPs<ref name=" Albrechtsen.2009"/>
* [http://people.binf.ku.dk/ida/Software/MCMC_IBDfinder/ MCMC_IBDfinder]: is based on [[Markov chain Monte Carlo]] (MCMC) for finding IBD segments in multiple individuals<ref name="Moltke.2011">{{Cite journal
| last1 = Moltke | first1 = I.
| last2 = Albrechtsen | first2 = A.
| last3 = Hansen | first3 = T. V. O.
| last4 = Nielsen | first4 = F. C.
| last5 = Nielsen | first5 = R.
| title = A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics
| doi = 10.1101/gr.115360.110
| journal = Genome Research
| volume = 21
| issue = 7
| pages = 1168–1180
| year = 2011
| pmid = 21493780
| pmc =3129259
}}</ref>
* [http://www.cs.ucla.edu/~danhe/Software/IBDGroupon.html IBD-Groupon]: detects group-wise IBD segments based on pairwise IBD relationships<ref name="He.2013">{{Cite journal
| last1 = He | first1 = D.
| title = IBD-Groupon: An efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships
| doi = 10.1093/bioinformatics/btt237
| journal = Bioinformatics
| volume = 29
| issue = 13
| pages = i162–i170
| year = 2013
| pmid = 23812980
| pmc =3694672
}}</ref>
* [http://www.bioinf.jku.at/research/short-IBD/ HapFABIA]: identifies very short IBD segments characterized by rare variants in large [[DNA sequencing|sequencing]] data simultaneously in multiple individuals<ref name="Hochreiter.2013"/>