LAIT: a local ancestry inference toolkit
Abstract 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 o...
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| Format: | Article |
| Language: | English |
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BMC
2017-09-01
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| Series: | BMC Genetics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12863-017-0546-y |
| _version_ | 1818008512286949376 |
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| author | Daniel Hui Zhou Fang Jerome Lin Qing Duan Yun Li Ming Hu Wei Chen |
| author_facet | Daniel Hui Zhou Fang Jerome Lin Qing Duan Yun Li Ming Hu Wei Chen |
| author_sort | Daniel Hui |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-14T05:31:17Z |
| format | Article |
| id | doaj.art-a0f93158109f4b679949e1d4d38d86bc |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-14T05:31:17Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-a0f93158109f4b679949e1d4d38d86bc2022-12-22T02:09:48ZengBMCBMC Genetics1471-21562017-09-011811510.1186/s12863-017-0546-yLAIT: a local ancestry inference toolkitDaniel Hui0Zhou Fang1Jerome Lin2Qing Duan3Yun Li4Ming Hu5Wei Chen6Department of Computer Science, University of PittsburghDepartment of Biostatistics, University of PittsburghDepartment of Human Genetics, University of PittsburghDepartment of Genetics, Curriculum in Bioinformatics and Computational Biology, Department of Statistics, Department of Computer Science, University of North CarolinaDepartment of Biostatistics, Department of Genetics, Department of Computer Science, University of North CarolinaDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland ClinicDepartment of Biostatistics, University of PittsburghAbstract 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.http://link.springer.com/article/10.1186/s12863-017-0546-yAdmixtureLocal ancestry inference |
| spellingShingle | Daniel Hui Zhou Fang Jerome Lin Qing Duan Yun Li Ming Hu Wei Chen LAIT: a local ancestry inference toolkit BMC Genetics Admixture Local ancestry inference |
| 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 | Admixture Local ancestry inference |
| url | http://link.springer.com/article/10.1186/s12863-017-0546-y |
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