Genetic mapping
Here are links to a number of Windows programs for genetic mapping using autozygosity or other approaches, that have been written by Ian Carr.
Affymetrix_Error_Rate
Affymetrix_Error_Rate finds the genotyping error rate and 'Nocall' genotype rate for Affymetrix microarray SNP chip genotype data. Affymetrix_Error_Rate web page
AgileGenotyper
AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data. AgileGenotyper page
AgileVariantMapper
AgileVariantMapper is part of the Agile suite of progams and is designed to visualise sequence variant data from whole exome data such that it is possible to identify autozygous regions in consanguineous individuals. The data can originate from files exported by AgileGenotyper, AgileAnnotator, AgileVariantViewer or a tab delimited text file formatted as described in the user guide webpage. AgileVariantMapper web page
AgileVCFMapper
AgileVCFMapper allows exome sequence variants in *.VCF files to be used to map disease loci in a similarly manner to AutoSNPa and IBDFinder. While it doesn't duplicate the functions of Phaser, Sample and DominantMapper, AgileVCFMapper can export the exome variant data to a coherent set of SNP genotype files that these programs can use.
AutoIdeogram
AutoIdeogram displays autozygous regions, identified in Affymetrix microarray SNP chip genotype data, against an ideogram of the human autosomal genome. AutoIdeogram web page
AgileMultiIdeogram
AgileMultiIdeogram displays autozygous regions from multiple individuals, identified in Affymetrix microarray SNP chip genotype data and/or exome variant data, against a circular ideogram of the human autosomal genome. AgileMultiIdeogram web page
AutoSNPa
AutoSNPa aids the identification of regions of Identity By Descent (IBD) in inbred families, by visually presenting colour-coded SNP genotype data ordered by physical or genetic distance. AutoSNPa web page
CNViewer
CNViewer aids the identification of regions of abnormal copy number variation that segregates with a disease phenotype in small pedigree. CNViewer web page
DominantMapper
DominantMapper is a method for identifying linkage to dominant genes in a single pedigree where there is SNP data for at least one pair of parents (one of whom is affected). Linkage information is then extrapolated from the genotypes of their affected and unaffected children as well as other affected relatives. DominantMapper web page
IBDelphi
IBDelphi is a program for identifying segments of Identity By Descent (IBD) between two individuals. Using this knowledge it is possible to calculate the coefficients of inbreeding and relationships, as well as the probability of one of their children suffering from an autosomal recessive disease, assuming their common ancestor is heterozygous for a deleterious mutation. IBDelphi web page
IBDfinder
IBDFinder aids the identification of regions of Identity By Descent (IBD) in inbred individuals, by plotting and collating runs of homozygous SNP genotypes, ordered by physical or genetic distance. IBDfinder web page
Phaser
Phaser is a program for the rapid identification of linkage to recessive disease genes in either consanguineous or out-bred families, by reconstructing the haplotype for each individual’s chromosomes within a pedigree. Phaser web page
SAMPLE
SAMPLE (“shadow” autozygosity mapping by linkage exclusion) is designed to identify regions that are linked to a recessive disease by analysing genotype data from the parents and unaffected sibs of affected individuals. Since this analysis does not use data from affected patients, it is suited to the identification of lethal recessive genes, when the patients may have died before DNA samples could be obtained. SAMPLE web page
SNPannotator
SNPannotator is designed to annotate the text output files from Affymetrix SNP 6.0 chips. These files are no longer annotated by the Affymetrix console, and so cannot be used by the other programs listed here. SNPannotator web page
SNPsetter
SNPsetter is a program for manipulating Affymetrix SNP metadata. SNPsetter will filter the SNPs exported, by chromosome, by allele frequency, or by distance from the last-exported SNP. While not always required when using AutoSNPa or IBDFinder, SNPsetter’s ability to collate SNP data from different chips may also be very useful when using these programs. SNPsetter web page
