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FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies

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, varian...

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Autores principales: Chung, Ren-Hua, Tsai, Wei-Yun, Kang, Chen-Yu, Yao, Po-Ju, Tsai, Hui-Ju, Chen, Chia-Hsiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894624/
https://www.ncbi.nlm.nih.gov/pubmed/27272119
http://dx.doi.org/10.1371/journal.pcbi.1004980
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author Chung, Ren-Hua
Tsai, Wei-Yun
Kang, Chen-Yu
Yao, Po-Ju
Tsai, Hui-Ju
Chen, Chia-Hsiang
author_facet Chung, Ren-Hua
Tsai, Wei-Yun
Kang, Chen-Yu
Yao, Po-Ju
Tsai, Hui-Ju
Chen, Chia-Hsiang
author_sort Chung, Ren-Hua
collection PubMed
description 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.
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spelling pubmed-48946242016-06-23 FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies Chung, Ren-Hua Tsai, Wei-Yun Kang, Chen-Yu Yao, Po-Ju Tsai, Hui-Ju Chen, Chia-Hsiang PLoS Comput Biol Research Article 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. Public Library of Science 2016-06-06 /pmc/articles/PMC4894624/ /pubmed/27272119 http://dx.doi.org/10.1371/journal.pcbi.1004980 Text en © 2016 Chung et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chung, Ren-Hua
Tsai, Wei-Yun
Kang, Chen-Yu
Yao, Po-Ju
Tsai, Hui-Ju
Chen, Chia-Hsiang
FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
title FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
title_full FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
title_fullStr FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
title_full_unstemmed FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
title_short FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
title_sort fampipe: an automatic analysis pipeline for analyzing sequencing data in families for disease studies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894624/
https://www.ncbi.nlm.nih.gov/pubmed/27272119
http://dx.doi.org/10.1371/journal.pcbi.1004980
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