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LAIT: a local ancestry inference toolkit
BACKGROUND: Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are available for inferring local ancestry in admixed individuals. However, most of these...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585928/ https://www.ncbi.nlm.nih.gov/pubmed/28877673 http://dx.doi.org/10.1186/s12863-017-0546-y |
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author | Hui, Daniel Fang, Zhou Lin, Jerome Duan, Qing Li, Yun Hu, Ming Chen, Wei |
author_facet | Hui, Daniel Fang, Zhou Lin, Jerome Duan, Qing Li, Yun Hu, Ming Chen, Wei |
author_sort | Hui, Daniel |
collection | PubMed |
description | BACKGROUND: Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are available for inferring local ancestry in admixed individuals. However, most of these existing software packages require specific formatted input files and generate output files in various types, yielding practical inconvenience. RESULTS: We developed a tool set, Local Ancestry Inference Toolkit (LAIT), which can convert standardized files into software-specific input file formats as well as standardize and summarize inference results for four popular local ancestry inference software: HAPMIX, LAMP, LAMP-LD, and ELAI. We tested LAIT using both simulated and real data sets and demonstrated that LAIT provides convenience to run multiple local ancestry inference software. In addition, we evaluated the performance of local ancestry software among different supported software packages, mainly focusing on inference accuracy and computational resources used. CONCLUSION: We provided a toolkit to facilitate the use of local ancestry inference software, especially for users with limited bioinformatics background. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0546-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5585928 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-55859282017-09-06 LAIT: a local ancestry inference toolkit Hui, Daniel Fang, Zhou Lin, Jerome Duan, Qing Li, Yun Hu, Ming Chen, Wei BMC Genet Software BACKGROUND: Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are available for inferring local ancestry in admixed individuals. However, most of these existing software packages require specific formatted input files and generate output files in various types, yielding practical inconvenience. RESULTS: We developed a tool set, Local Ancestry Inference Toolkit (LAIT), which can convert standardized files into software-specific input file formats as well as standardize and summarize inference results for four popular local ancestry inference software: HAPMIX, LAMP, LAMP-LD, and ELAI. We tested LAIT using both simulated and real data sets and demonstrated that LAIT provides convenience to run multiple local ancestry inference software. In addition, we evaluated the performance of local ancestry software among different supported software packages, mainly focusing on inference accuracy and computational resources used. CONCLUSION: We provided a toolkit to facilitate the use of local ancestry inference software, especially for users with limited bioinformatics background. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0546-y) contains supplementary material, which is available to authorized users. BioMed Central 2017-09-06 /pmc/articles/PMC5585928/ /pubmed/28877673 http://dx.doi.org/10.1186/s12863-017-0546-y Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Hui, Daniel Fang, Zhou Lin, Jerome Duan, Qing Li, Yun Hu, Ming Chen, Wei LAIT: a local ancestry inference toolkit |
title | LAIT: a local ancestry inference toolkit |
title_full | LAIT: a local ancestry inference toolkit |
title_fullStr | LAIT: a local ancestry inference toolkit |
title_full_unstemmed | LAIT: a local ancestry inference toolkit |
title_short | LAIT: a local ancestry inference toolkit |
title_sort | lait: a local ancestry inference toolkit |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585928/ https://www.ncbi.nlm.nih.gov/pubmed/28877673 http://dx.doi.org/10.1186/s12863-017-0546-y |
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