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. 2020 Sep 18;15(9):e0239144.
doi: 10.1371/journal.pone.0239144. eCollection 2020.

coPLINK: A complementary tool to PLINK

Han-Ming Liu  1 , Zhao-Fa Liu  1 , Jin-Ping Zheng  1 , Dan Yang  1 , Sheng-Zhou Hu  1 , Shen-Hai Yan  1 , Xian-Wen He  1
Affiliations

coPLINK: A complementary tool to PLINK

Han-Ming Liu et al. PLoS One. .

Abstract

In genome-wide association studies (GWAS), a wide variety of analysis tools have been designed, leading to various formats of GWAS data. How to convert a dataset in non-PLINK format into PLINK format to use its powerful analysis performance, or to convert a dataset in PLINK format into the format of other analysis tools, is a problem that needs to be faced and solved. To address this issue, we developed a tool called coPLINK, a complementary tool to PLINK, to cooperate with PLINK to implement the conversions of GWAS data formats and to provide some additional functions, such as data files comparison. The tool can implement mutual conversions not only between an existing data format and PLINK PED/BED, but also between a user-defined data format and PLINK PED. The usage and performance of the tool are similar to PLINK. The characteristics of the conversions of existing data formats and user-defined formats make it be a good assistant to PLINK or other tools and, have good potential for GWAS studies or other works.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Example of converting PLINK PED to user-defined format.
The files Other.geo and Other.txt are space delimited (more spaces were added for readability), and the Other.snp is tab delimited. The delimiter in the arguments files is a comma which can be ignored if there are no more items such as “Sex, 2” in Arguments file 2. The MATRIX section describes the components of the genotype matrix while the VECTOR section gives the other components of the data, and the INSERT section provides how to insert additional rows/columns.
Fig 2
Fig 2. Elapsed time and peak memory of coPLINK.
See this image and copyright information in PMC

References

    1. Klein RJ, Zeiss C, Chew EY, Tsai J-Y, Sackler RS, Haynes C, et al. Complement factor H polymorphism in age-related macular degeneration. Science. 2005;308(5720):385–9. 10.1126/science.1109557 - DOI - PMC - PubMed
    1. Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, et al. 10 years of GWAS discovery: biology, function, and translation. The American Journal of Human Genetics. 2017;101(1):5–22. 10.1016/j.ajhg.2017.06.005 - DOI - PMC - PubMed
    1. Lee S-H, Park B-H, Sharma A, Dang C-G, Lee S-S, Choi T-J, et al. Hanwoo cattle: origin, domestication, breeding strategies and genomic selection. Journal of animal science and technology. 2014;56(1):2. - PMC - PubMed
    1. Su J, Jiang J, Zhang F, Liu Y, Ding L, Chen S, et al. Current achievements and future prospects in the genetic breeding of chrysanthemum: a review. Horticulture research. 2019;6(1):1–19. - PMC - PubMed
    1. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics. 2007;81(3):559–75. 10.1086/519795 - DOI - PMC - PubMed

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