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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   

•   Source: SciCrunch Registry

https://www.sfari.org/funding-opportunities/

The mission of SFARI is to improve the diagnosis, treatment, and prevention of autism and related developmental disorders. SFARI explores neuroscience from multiple directions, including molecular, cellular, systems, immunological, cognitive, behavioral, genetic, theoretical and computational perspectives. Funding for innovative scientific research is available through a peer-reviewed proposal process at regular intervals. Research projects are reviewed by a scientific advisory board and managed by the scientific director and a highly qualified staff. Proposals in multiple research areas are sought, to reflect the complex nature of autism. The Foundation supports innovative scientific projects where our involvement will play an essential role. In the course of this support, The Foundation is interested in partnering with other entities, or providing matching support where appropriate. The Simons Foundation has historically accepted only solicited grant proposals. These grant decisions are made by the Trustees of The Simons Foundation, who review applications on an ongoing basis. In the area of autism research, requests for proposals are issued on an annual basis. The Simons Foundation does not give grants to individuals, except through their institutions.

Proper citation: Simons Foundation Autism Research Initiative: Grant Resource (RRID:SCR_001862) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LAMBDAA (RRID:SCR_001128) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/carol

Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

Proper citation: CAROL (RRID:SCR_001800) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LDMET (RRID:SCR_001127) Copy   

•   Source: SciCrunch Registry

http://support.illumina.com/sequencing/sequencing_software/casava.html

Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

Proper citation: CASAVA (RRID:SCR_001802) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Polymutt

Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software)

Proper citation: POLYMUTT (RRID:SCR_002051) Copy   

•   Source: SciCrunch Registry

https://hsph.harvard.edu/research/price-lab/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/birdsuite/birdsuite

Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

Proper citation: BIRDSUITE (RRID:SCR_001794) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/dindel

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Proper citation: DINDEL (RRID:SCR_001827) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/pedigraph/

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy   

•   Source: SciCrunch Registry

http://ftp://morgan.med.utah.edu/pub/Mim

Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software)

Proper citation: Multipoint Identical-by-descent Method (RRID:SCR_004676) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/PedScript

Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software)

Proper citation: PEDSCRIPT (RRID:SCR_004571) Copy   

•   Source: SciCrunch Registry

http://www.chg.duke.edu/software/pedplot.html

Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software)

Proper citation: PEDPLOT (RRID:SCR_003843) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/hapmixmap/hapmixmap_manual.html

Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software)

Proper citation: HAPMIXMAP (RRID:SCR_006066) Copy   

•   Source: SciCrunch Registry

http://www2.ujf-grenoble.fr/leca/membres/manel.html

Software application for parentage inference using molecular data from diploid codominant markers (entry from Genetic Analysis Software)

Proper citation: PARENTE (RRID:SCR_004717) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software)

Proper citation: PEDRAW/WPEDRAW (RRID:SCR_004797) Copy   

•   Source: SciCrunch Registry

http://biostatistics.mdanderson.org/SoftwareDownload/

Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software)

Proper citation: TDTASP (RRID:SCR_004943) Copy   

•   Source: SciCrunch Registry

http://ki.se/en/meb/twingene-and-genomeeutwin

In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed)

Proper citation: KI Biobank - TwinGene (RRID:SCR_006006) Copy   

•   Source: SciCrunch Registry

http://genomics.med.upenn.edu/spielman/TDT.htm

Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software)

Proper citation: TDT/S-TDT (RRID:SCR_005548) Copy   

•   Source: SciCrunch Registry