ArticleBioinformatics (Oxford, England)2014
Cosi2: an efficient simulator of exact and approximate coalescent with selection.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
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- Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.PLoS computational biology · 2023Article
- Ultrafast genome-wide inference of pairwise coalescence times.Genome research · 2023Article
- Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity.Microbiome · 2023Article
- Accommodating multiple potential normalizations in microbiome associations studies.BMC bioinformatics · 2023Article
- Demes: a standard format for demographic models.Genetics · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Simultaneous detection of novel genes and SNPs by adaptiveFrontiers in genetics · 2022Article
- Genomic Targets of Positive Selection in Giant Mice from Gough Island.Molecular biology and evolution · 2021Article
- Quantitative phenotype scan statistic (QPSS) reveals rare variant associations with Alzheimer's disease endophenotypes.BMC medical genetics · 2020Article
- Exploration of fine-scale recombination rate variation in the domestic horse.Genome research · 2019Article
- Genetic Variation in Human Gene Regulatory Factors Uncovers Regulatory Roles in Local Adaptation and Disease.Genome biology and evolution · 2019Article
- POPdemog: visualizing population demographic history from simulation scripts.Bioinformatics (Oxford, England) · 2018Article
- The Weighting is the Hardest Part: On the Behavior of the Likelihood Ratio Test and the Score Test Under a Data-Driven Weighting Scheme in Sequenced Samples.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationEfficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection. Gene conversion is not supported by any published coalescent simulators that support selection.
resultsWe describe cosi2, an efficient simulator that supports both exact and approximate coalescent simulation with positive selection. cosi2 improves on the speed of existing exact simulators, and permits further speedup in approximate mode while retaining support for selection. cosi2 supports a wide range of demographic scenarios, including recombination hot spots, gene conversion, population size changes, population structure and migration. cosi2 implements coalescent machinery efficiently by tracking only a small subset of the Ancestral Recombination Graph, sampling only relevant recombination events, and using augmented skip lists to represent tracked genetic segments. To preserve support for selection in approximate mode, the Markov approximation is implemented not by moving along the chromosome but by performing a standard backwards-in-time coalescent simulation while restricting coalescence to node pairs with overlapping or near-overlapping genetic material. We describe the algorithms used by cosi2 and present comparisons with existing selection simulators. AVAILABILITY AND IMPLEMENTATION: A free C++ implementation of cosi2 is available at http://broadinstitute.org/mpg/cosi2.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.