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
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.
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.
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.
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 .
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
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.
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.