MultiGeMS specifications


Unique identifier OMICS_11067
Name MultiGeMS
Alternative name Multi-sample Genotype Model Selection
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data MultiGeMS accepts a text file, listing on separate lines, paths of SAMtools pileup format files. To convert a SAM/BAM alignment file into the pileup format, users can use the SAMtools mpileup procedure with option -s.
Output data The MultiGeMS output is similar to that of the Variant Call Format (VCF) file format. Meta-information lines are provided at the beginning of each output. Only sites less than the user-selected lFDR SNV threshold are output and are considered SNV calls.
Operating system Unix/Linux
Programming languages C++
Parallelization OpenMP
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes


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  • person_outline Xinping Cui <>

MultiGeMS article

MultiGeMS institution(s)
Department of Statistics, University of California, Riverside, CA, USA; Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, Guangdong, China; Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
MultiGeMS funding source(s)
This work was supported by the National Science Foundation [ATD-1222718]; the University of California, Riverside [AES-CE RSAP A01869]; R01HG113147; the National Science Foundation of China [NSFC 11301554, NSFC 61103167, 31271410, 31401076]; the Ministry of Science and Technology [high-tech (863) grant 2012AA023107, 2014AA021502]; the Sino-German Research Center [GZ878]; and the Huazhong University of Science and Technology [start-up fund].

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