Please use this identifier to cite or link to this item:
https://hdl.handle.net/1959.11/17692
Title: | SNPQC: an R pipeline for quality control of Illumina SNP genotyping array data | Contributor(s): | Gondro, Cedric (author) ; Porto-Neto, Laércio R (author); Lee, Seung Hwan (author) | Publication Date: | 2014 | DOI: | 10.1111/age.12198 | Handle Link: | https://hdl.handle.net/1959.11/17692 | Abstract: | In genome-wide association studies, quality control (QC) of genotypes is important to avoid spurious results. It is also important to maintain long-term data integrity, particularly in settings with ongoing genotyping (e.g. estimation of genomic breeding values). Here we discuss SNPQC, a fully automated pipeline to perform QC analyses of Illumina SNP array data. It applies a wide range of common quality metrics with user-defined filtering thresholds to generate a comprehensive QC report and a filtered dataset, including a genomic relationship matrix, ready for further downstream analyses which make it amenable for integration in high-throughput environments. SNPQC also builds a database to store genotypic, phenotypic and quality metrics to ensure data integrity and the option of integrating more samples from subsequent runs. The program is generic across species and array designs, providing a convenient interface between the genotyping laboratory and downstream genome-wide association study or genomic prediction. | Publication Type: | Journal Article | Source of Publication: | Animal Genetics, 45(5), p. 758-761 | Publisher: | Wiley-Blackwell Publishing Ltd | Place of Publication: | United Kingdom | ISSN: | 1365-2052 0268-9146 |
Fields of Research (FoR) 2008: | 060408 Genomics 070201 Animal Breeding |
Fields of Research (FoR) 2020: | 310509 Genomics 300305 Animal reproduction and breeding |
Socio-Economic Objective (SEO) 2008: | 970106 Expanding Knowledge in the Biological Sciences | Socio-Economic Objective (SEO) 2020: | 280102 Expanding knowledge in the biological sciences | Peer Reviewed: | Yes | HERDC Category Description: | C1 Refereed Article in a Scholarly Journal |
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Appears in Collections: | Journal Article |
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