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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Bibliographic Details
Published in:PLoS computational biology 2016-06, Vol.12 (6), p.e1004980-e1004980
Main Authors: Chung, Ren-Hua, Tsai, Wei-Yun, Kang, Chen-Yu, Yao, Po-Ju, Tsai, Hui-Ju, Chen, Chia-Hsiang
Format: Article
Language:English
Subjects:
Automation
Biology and Life Sciences
Computational Biology
Computer Simulation
Design
Disease
DNA sequencing
Families & family life
Genetic Association Studies
Genetic Predisposition to Disease - genetics
High-Throughput Nucleotide Sequencing - methods
Humans
Internet
Methods
Mutation
Performance evaluation
Research and Analysis Methods
Sequence Analysis, DNA - methods
Software
Studies
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Summary: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.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1004980