Document Detail


snpqc - an R pipeline for quality control of Illumina SNP genotyping array data.
MedLine Citation:
PMID:  25040453     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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.
Authors:
Cedric Gondro; Laercio R Porto-Neto; Seung Hwan Lee
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2014-7-18
Journal Detail:
Title:  Animal genetics     Volume:  -     ISSN:  1365-2052     ISO Abbreviation:  Anim. Genet.     Publication Date:  2014 Jul 
Date Detail:
Created Date:  2014-7-21     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8605704     Medline TA:  Anim Genet     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
© 2014 Stichting International Foundation for Animal Genetics.
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