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Title: SNPQC: an R pipeline for quality control of Illumina SNP genotyping array data
Contributor(s): Gondro, Cedric  (author)orcid ; Porto-Neto, Laércio R (author); Lee, Seung Hwan (author)
Publication Date: 2014
DOI: 10.1111/age.12198
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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: 0268-9146
Field of Research (FOR): 060408 Genomics
070201 Animal Breeding
Socio-Economic Outcome Codes: 970106 Expanding Knowledge in the Biological Sciences
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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