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, 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.
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
Ren-Hua
RH
Chung
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
Wei-Yun
WY
Tsai
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
Chen-Yu
CY
Kang
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
Po-Ju
PJ
Yao
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.|Department of Public Health, China Medical University, Taichung, Taiwan.|Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.
Hui-Ju
HJ
Tsai
Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Gueishan, Taoyuan, Taiwan.|Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
Chia-Hsiang
CH
Chen
D019295:Computational Biology; D003198:Computer Simulation; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software