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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
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
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
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
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
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
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
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
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