Literature DB >> 19346322

IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.

Miao-Xin Li1, Lin Jiang, Patrick Yu-Ping Kao, Pak-C Sham, You-Qiang Song.   

Abstract

SUMMARY: There is an urgent and increasing demand for integrating large genotype datasets across genome-wide association studies and HapMap project for whole-genome imputation and individual-level meta-analysis. A new algorithm was developed to efficiently merge raw genotypes across large datasets and implemented in the latest version of IGG, IGG3. In addition, IGG3 can integrate the latest phased and unphased HapMap genotypes and can flexibly generate complete sets of input files for six popular genotype imputation tools. We demonstrated the efficiency of IGG3 by simulation tests, which could rapidly merge genotypes in tens of thousands of large genotype chips (e.g. Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina Human1m-duo) and in HapMap III project on an ordinary desktop computer. AVAILABILITY: (http://bioinfo.hku.hk/iggweb) (version 3.0).

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Mesh：

Year:  2009        PMID： 19346322     DOI： 10.1093/bioinformatics/btp183

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

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4.  Assessment of common variability and expression quantitative trait loci for genome-wide associations for progressive supranuclear palsy.

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Review 5.  Rising Strengths Hong Kong SAR in Bioinformatics.

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6.  Impact of pre- and post-variant filtration strategies on imputation.

Authors:  Céline Charon; Rodrigue Allodji; Vincent Meyer; Jean-François Deleuze
Journal:  Sci Rep       Date:  2021-03-18       Impact factor: 4.379

7.  Genome-wide association analysis with gray matter volume as a quantitative phenotype in first-episode treatment-naïve patients with schizophrenia.

Authors:  Qiang Wang; Bo Xiang; Wei Deng; Junyao Wu; Mingli Li; Xiaohong Ma; Yingcheng Wang; Lijun Jiang; Grainne McAlonan; Siew E Chua; Pak C Sham; Xun Hu; Tao Li
Journal:  PLoS One       Date:  2013-09-24       Impact factor: 3.240
  7 in total

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