Genotypes
This script converts categorical genotypes such as AA, AG without a delimiter to the standard genotype format accepted by Golden Helix SVS (A_A, A_G, etc). The script prompts for the missing value indicator. Possible uses include converting genotype columns after importing data that were...
Platforms: Mac
License: Freeware | Size: 10.24 KB | Download (44): Add Allele Delimiter Download |
This script takes genotypes from two different arrays and creates a consensus spreadsheet, and two optional spreadsheets. In order to run this script two spreadsheets of mapped genotype data are required. The spreadsheets may also contain non-marker mapped columns as they will be skipped when...
Platforms: Mac
License: Freeware | Size: 10.24 KB | Download (42): Consensus and Combination of Two Arrays Download |
A simple java application that creates punnett squares for given parent genotypes.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 74.39 KB | Download (45): Punnett Square Caclulator Download |
This script recodes AGCT alleles to the standard genotype format of A_A, A_B, and B_B. Prompts for a marker map strand field to use for recoding. The strand field must have allele information in the form [C/T]. Missing genotypes remain missing.
Platforms: Mac
License: Freeware | Size: 46.08 KB | Download (36): Recode AGCT Alleles to AB Download |
This script imports multiple fields of data from Illumina Final Report text files. It can be used to just import genotype data, or multiple real-valued columns such as B-Allele Frequency, or Log R Ratios. The user can choose from all fields found in the text file and select which ones should be...
Platforms: Mac
License: Freeware | Size: 10.24 KB | Download (34): Import Illumina Text File Download |
What is snpEff? It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs). Release Candidate 1 Take a look at all the new features added Database download command, e.g. "java -jar snpEff.jar download GRCH37.64" RefSeq annotations...
Platforms: Mac
License: Freeware | Size: 3.73 MB | Download (37): snpEff Download |
UNPHASED is a small, simple, Java based application specially designed to offer users a versatile tool for performing genetic association analysis.
This utility implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes....
Platforms: Windows
License: Freeware | Download (391): UNPHASED Download |
Open BEAGLE is a C Evolutionary Computation (EC) framework. It provides an high-level software environment to do any kind of EC, with support for tree-based genetic programming; bit string, integer-valued vector, and real-valued vector genetic algorithms; and evolution strategy.The Open BEAGLE...
Platforms: Windows, Mac, *nix, C/C++, BSD Solaris
License: Freeware | Download (59): Open BEAGLE Download |