國家衛生研究院 NHRI:Item 3990099045/9815
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/9815


    Title: FamPipe: An automatic analysis pipeline for analyzing sequencing data in families for disease studies
    Authors: Chung, RH;Tsai, WY;Kang, CY;Yao, PJ;Tsai, HJ;Chen, CH
    Contributors: Division of Biostatistics and Bioinformatics
    Abstract: In disease studies, family-based designs have become an attractive approach to analyzing next-generation sequencing (NGS) data for the identification of rare mutations enriched in families. Substantial research effort has been devoted to developing pipelines for automating sequence alignment, variant calling, and annotation. However, fewer pipelines have been designed specifically for disease studies. Most of the current analysis pipelines for family-based disease studies using NGS data focus on a specific function, such as identifying variants with Mendelian inheritance or identifying shared chromosomal regions among affected family members. Consequently, some other useful family-based analysis tools, such as imputation, linkage, and association tools, have yet to be integrated and automated. We developed FamPipe, a comprehensive analysis pipeline, which includes several family-specific analysis modules, including the identification of shared chromosomal regions among affected family members, prioritizing variants assuming a disease model, imputation of untyped variants, and linkage and association tests. We used simulation studies to compare properties of some modules implemented in FamPipe, and based on the results, we provided suggestions for the selection of modules to achieve an optimal analysis strategy. The pipeline is under the GNU GPL License and can be downloaded for free at http://fampipe.sourceforge.net.
    Date: 2016-06
    Relation: PLoS Computational Biology. 2016 Jun;12(6):Article number e1004980.
    Link to: http://dx.doi.org/10.1371/journal.pcbi.1004980
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=1553-734X&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000379349700049
    Cited Times(Scopus): http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84978864803
    Appears in Collections:[Ren-Hua Chung] Periodical Articles
    [Hui-Ju Tsai] Periodical Articles

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