link-ancestors: fast simulation of local ancestry with tree sequence software

SUMMARY: It is challenging to simulate realistic tracts of genetic ancestry on a scale suitable for simulation-based inference. We present an algorithm that enables this information to be extracted efficiently from tree sequences produced by simulations run with msprime and SLiM. AVAILABILITY AND IM...

Descripción completa

Detalles Bibliográficos
Autores principales: Tsambos, Georgia, Kelleher, Jerome, Ralph, Peter, Leslie, Stephen, Vukcevic, Damjan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Application Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10682689/
https://www.ncbi.nlm.nih.gov/pubmed/38033661
http://dx.doi.org/10.1093/bioadv/vbad163
Descripción
Sumario:SUMMARY: It is challenging to simulate realistic tracts of genetic ancestry on a scale suitable for simulation-based inference. We present an algorithm that enables this information to be extracted efficiently from tree sequences produced by simulations run with msprime and SLiM. AVAILABILITY AND IMPLEMENTATION: A C-based implementation of the link-ancestors algorithm is in tskit (https://tskit.dev/tskit/docs/stable/). We also provide a user-friendly wrapper for link-ancestors in tspop, a Python-based utility package.

Ejemplares similares