Software

ATAV
ATAV (Analysis Tool for Annotated Variants) is a statistical toolset that is designed to detect complex disease-associated rare genetic variants by performing association analysis on annotated variants derived from whole-genome or whole-exome sequencing data.
 
RVIS
RVIS (Residual Variation Intolerance Score) is a gene-based score intended to help in the interpretation of human sequence data.  The intolerance score in its current form is based upon allele frequency data as represented in whole exome sequence data from the NHLBI-ESP6500 data set.  The score is designed to rank genes in terms of whether they have more or less common functional genetic variation relative to the genome wide expectation given the amount of apparently neutral variation the gene has.  A gene with a positive score has more common functional variation, and a gene with a negative score has less and is referred to as "intolerant".   By convention we rank all genes in order from most intolerant to least.  As an example, a gene such as ATP1A3 has a RVIS score of -1.53 and a percentile of 3.37%, meaning it is amongst the 3.37% most intolerant of human genes.  Depending on what disease area you are a studying, you may way to consider either intolerant genes (neurodevelomental disease) or tolerant genes (some immunological diseases) as better candidates.
 
ERDS
ERDS is designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data, utilizing information from read depth of short reads and SNV heterozygosity.
 
WGAViewer
WGAViewer is a bioinformatic software tool specifically designed to provide a user-friendly interface to automatically annotate, visualize, and interpret the set of P values emerging from a GWAS study. It can be used to highlight possible functional mechanisms, to help create working hypothesis, and to select genomic regions that may need to be resequenced in a search for candidate causal variants.
 
MetaP
MetaP performs a meta-analysis and combines the statistical association signals (P values) from independent studies or study populations, taking account of the impacts of sample sizes and effect directions.
 
SNPExpress
SNPExpress is a database interface that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression. This database enables researchers to input a SNP, gene, or a genomic region to investigate regions of interest for localized effects of SNPs on exon and gene level expression changes.
 
GWASpower/QT
GWASpower/QT is a statistical power calculation software designed for genome wide association studies (GWAS) with quantitative traits in natural populations. It allows users to input the effect size as heritability measures, instead of the phenotype means of each genotype of the genetic marker, which is often unavailable in exploratory experiments such as GWAS. Input parameters are heritability (required), type 1 error rate (required), total sample size (required), linkage disequilibrium (optional) and other covariates (optional). The software returns the statistical power and a plot of a family of power curves. Documentation.
 
DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data. It can be used as either a stand-alone tool to detect DNM or coupled with other commonly used DNM detection tool (GATK UnifiledGenotyper, polymutt, DenovoGear et al.) to improve specificity.
 

 

 

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