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Michigan Imputation Server provides a free genotype imputation service. You can upload GWAS genotypes (VCF or 23andMe format) and receive phased and imputed genomes in return. The server offers imputation from HapMap, 1000 Genomes (Phase 1 and 3), CAAPA and the updated Haplotype Reference Consortium (HRC version r1.1) panel.

https://imputationserver.sph.umich.edu


mtDNA-Server provides a free service for the analysis of human mitochondrial DNA data, currently focusing on reliable identification of heteroplasmy (>= 1%) and contamination. mtDNA-Server can be executed without any user login. We also provide post-processing guidelines that should be applied after each automated analysis.

https://mtdna-server.uibk.ac.at/

 


 

HaploGrep is a web application for finding the corresponding haplogroup to given mtDNA profiles based on Phylotree (mtDNA classification tree). Any given range of the mitochondrial genome can be used for haplogroup classification, which is based on the phylogenetic stability of mtDNA polymorphisms. HaploGrep generates an interactive data visualization of the results and provides recommendations which polymorphisms should be analyzed additionally to get a more accurate result.

http://haplogrep.uibk.ac.at/

Paper: HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups http://onlinelibrary.wiley.com/doi/10.1002/humu.21382/full
Paper: HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing https://academic.oup.com/nar/article/44/W1/W58/2499296/HaploGrep-2-mitochondrial-haplogroup

 


 

SNPflow is a freely available web application to automatically check the quality of SNP data employing the ABI 7900 HT-platform (e.g. TaqMan, KASPar Assays) or the Sequenom iPLEX platform: Single raw output files of plates are automatically merged and converted to genotype lists. Furthermore, calculation of call rates, discordance rates, Hardy Weinberg Equilibrium (HWE) and a comparison with data from the HapMap project are automatically accomplished.

http://www.genepi-snpflow.i-med.ac.at/

Paper: SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059508

 


 

CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes. Moreover, CONAN assists the evaluation process by visualizing detected associations via Manhattan plots in order to enable a rapid identification of genome-wide significant CNV regions. Various file formats including the information on CNVs in population samples are supported as input data.

http://genepi-conan.i-med.ac.at/
Paper: CONAN: copy number variation analysis software for genome-wide association studies http://www.biomedcentral.com/1471-2105/11/318

 


 

eCOMPAGT is an application for the efficient COmbination and Management of Phenotypes. eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data. Furthermore eCOMPAGT was designed to enable error‐free post‐laboratory data handling of human mtDNA profiles.

http://dbis-informatik.uibk.ac.at/ecompagt

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