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http://www.yandell-lab.org/software/vaast.html
A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases.
Proper citation: VAAST (RRID:SCR_002179) Copy
http://sift.bii.a-star.edu.sg/
Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.
Proper citation: SIFT (RRID:SCR_012813) Copy
http://www.omicsexpress.com/sva.php
Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.
Proper citation: SVA (RRID:SCR_002155) Copy
https://reich.hms.harvard.edu/software
Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.
Proper citation: Ancestrymap (RRID:SCR_004353) Copy
http://www.nhlbi.nih.gov/guidelines/obesity/BMI/bmicalc.htm
Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women.
Proper citation: Body Mass Index Calculator (RRID:SCR_000122) Copy
http://www.homozygositymapper.org/
A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)
Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy
http://eyegene.ophthy.med.umich.edu/madeline/
Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.
Proper citation: MADELINE (RRID:SCR_001979) Copy
http://www.sph.umich.edu/csg/abecasis/GOLD/
Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.
Proper citation: Graphical Overview of Linkage Disequilibrium (RRID:SCR_007151) Copy
http://www.openbioinformatics.org/annovar/
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 can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)
Proper citation: ANNOVAR (RRID:SCR_012821) Copy
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