:: DESCRIPTION
The SPrime program identifies variants that are introgressed from archaic populations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhou Y, Browning SR.
Protocol for detecting introgressed archaic variants with SPrime.
STAR Protoc. 2021 May 19;2(2):100550. doi: 10.1016/j.xpro.2021.100550. PMID: 34095864; PMCID: PMC8164089.
:: DESCRIPTION
Motif-Raptor, a TF-centric computational tool that integrates sequence-based predic-tive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yao Q, Ferragina P, Reshef Y, Lettre G, Bauer DE, Pinello L.
Motif-Raptor: A Cell Type-Specific and Transcription Factor Centric Approach for Post-GWAS Prioritization of Causal Regulators.
Bioinformatics. 2021 Feb 3:btab072. doi: 10.1093/bioinformatics/btab072. Epub ahead of print. PMID: 33532840.
:: DESCRIPTION
SNiPA offers both functional annotations and linkage disequilibrium information for bi-allelic genomic variants (SNPs and SNVs). SNiPA combines LD data based on the 1000 Genomes Project with various annotation layers, such as gene annotations, phenotypic trait associations, and expression-/metabolic quantitative trait loci.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SNiPA: an interactive, genetic variant-centered annotation browser.
Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmüller G.
Bioinformatics. 2014 Nov 26. pii: btu779
:: DESCRIPTION
GREGOR (Genomic Regulatory Elements and Gwas Overlap algoRithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GREGOR: Evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach.
Schmidt EM, Zhang J, Zhou W, Chen J, Mohlke KL, Chen YE, Willer CJ.
Bioinformatics. 2015 Apr 16. pii: btv201.
:: DESCRIPTION
HMMvar: Small indels account for the second largest portion of human variants, however, available methods for indel functional predictions, no matter in coding or noncoding regions, are many fewer compared to those for SNPs. We developed HMMvar for predicting the functional effects of both SNPs and indels in coding regions of sequences.
HMMvar-multi: Complex diseases are likely to be caused by multiple genes and/or multiple mutations on individual genes, so quantitively measuring the effect of multiple variants together should be helpful for detecting causal genes/mutations for diseases. HMMvar-multi predicts the functional effects of multiple variants in the same gene based on HMMvar.
HMMvar-func is a new method for predicting the functional outcome of mutations in coding regions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
HMMvar / HMMvar-multi / HMMvar-func
:: MORE INFORMATION
Citation
Liu M, Watson LT, Zhang L.
Predicting the combined effect of multiple genetic variants.
Hum Genomics. 2015 Jul 30;9(1):18. doi: 10.1186/s40246-015-0040-4. PMID: 26223264; PMCID: PMC4520001.
BMC Bioinformatics. 2015 Oct 30;16:351. doi: 10.1186/s12859-015-0781-z.
HMMvar-func: a new method for predicting the functional outcome of genetic variants.
Liu M, Watson LT, Zhang L.
:: DESCRIPTION
Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology .
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Narzisi G, O’Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.
Nat Methods. 2014 Oct;11(10):1033-6. doi: 10.1038/nmeth.3069.
:: DESCRIPTION
DANN is a deep learning approach for annotating the pathogenicity of genetic variants.
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Quang D, Chen Y, Xie X.
Bioinformatics. 2015 Mar 1;31(5):761-3. doi: 10.1093/bioinformatics/btu703.
:: DESCRIPTION
ANNOVAR (ANNOtation of genetic VARiants) is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Wang K, Li M, Hakonarson H.
ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data
Nucleic Acids Research, 38:e164, 2010
:: DESCRIPTION
ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. wANNOVAR provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software, to facilitate biologists without bioinformatics skills taking full advantage of the sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
J Med Genet. 2012 Jul;49(7):433-6. doi: 10.1136/jmedgenet-2012-100918. Epub 2012 Jun 20.
wANNOVAR: annotating genetic variants for personal genomes via the web.
Chang X1, Wang K.
:: DESCRIPTION
FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Haplotype-based variant detection from short-read sequencing
Erik Garrison, Gabor Marth