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GIGI-Quick: a fast approach to impute missing genotypes in genome-wide association family data.

TitleGIGI-Quick: a fast approach to impute missing genotypes in genome-wide association family data.
Publication TypeJournal Article
Year of Publication2018
AuthorsKunji K, Ullah E, Nato AQ, Wijsman EM, Saad M
JournalBioinformatics
Volume34
Issue9
Pagination1591-1593
Date Published2018 05 01
ISSN1367-4811
KeywordsGenome-Wide Association Study, Genotype, Pedigree, Software
Abstract

Summary: Genome-wide association studies have become common over the last ten years, with a shift towards targeting rare variants, especially in pedigree-data. Despite lower costs, sequencing for rare variants still remains expensive. To have a relatively large sample with acceptable cost, imputation approaches may be used, such as GIGI for pedigree data. GIGI is an imputation method that handles large pedigrees and is particularly good for rare variant imputation. GIGI requires a subset of individuals in a pedigree to be fully sequenced, while other individuals are sequenced only at relevant markers. The imputation will infer the missing genotypes at untyped markers. Running GIGI on large pedigrees for large numbers of markers can be very time consuming. We present GIGI-Quick as a method to efficiently split GIGI's input, run GIGI in parallel and efficiently merge the output to reduce the runtime with the number of cores. This allows obtaining imputation results faster, and therefore all subsequent association analyses.
Availability and and implementation: GIGI-Quick is open source and publicly available via: https://cse-git.qcri.org/Imputation/GIGI-Quick.
Contact: msaad@hbku.edu.qa.
Supplementary information: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btx782
Pubmed Linkhttps://www.ncbi.nlm.nih.gov/pubmed/29267877?dopt=Abstract
page_expoExternal
Alternate JournalBioinformatics
PubMed ID29267877
PubMed Central IDPMC5925782
Grant ListR37 GM046255 / GM / NIGMS NIH HHS / United States
U01 AG049507 / AG / NIA NIH HHS / United States
R01 GM046255 / GM / NIGMS NIH HHS / United States
R01 HD088431 / HD / NICHD NIH HHS / United States
P50 AG005136 / AG / NIA NIH HHS / United States
R01 MH094293 / MH / NIMH NIH HHS / United States

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