TY - JOUR
T1 - LAIT
T2 - A local ancestry inference toolkit
AU - Hui, Daniel
AU - Fang, Zhou
AU - Lin, Jerome
AU - Duan, Qing
AU - Li, Yun
AU - Hu, Ming
AU - Chen, Wei
N1 - Publisher Copyright:
© 2017 The Author(s).
PY - 2017/9/6
Y1 - 2017/9/6
N2 - 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.
AB - 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.
KW - Admixture
KW - Local ancestry inference
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U2 - 10.1186/s12863-017-0546-y
DO - 10.1186/s12863-017-0546-y
M3 - Article
C2 - 28877673
AN - SCOPUS:85028929590
SN - 1471-2156
VL - 18
JO - BMC genetics
JF - BMC genetics
IS - 1
M1 - 83
ER -