Homozygosity mapping software tools | Whole-exome sequencing data analysis
Homozygosity defines a gene that is represented by two identical alleles on both homologous chromosomes. When the two alleles originate from a common ancestor, the genotype is said to be autozygous. Homozygosity mapping is a common method for mapping recessive traits in consanguineous families. Homozygosity and autozygosity mapping software tools use high-throughput technologies such as whole-exome sequencing or SNPs data to identify homozygous regions.
A web-based application aimed at autozygosity mapping. HomozygosityMapper is independent of parameters like family structure or allele frequencies, the ‘homozygosity score’ is calculated simply from the observed homozygosity and it is robust against genotyping errors. HomozygosityMapper is much faster than conventional linkage software. The integration with GeneDistiller greatly facilitates the search for promising candidate genes compared to the conventional approach. We also encourage geneticists to consider HomozygosityMapper as a public repository for genotypes and results when publishing their homozygosity mappings. Due to its user-friendly intuitive interface and the lack of any local hardware requirements, it can be used by the geneticists themselves without the need for computer specialists.
An approach for the detection of runs of homozygosity from individual whole-exome sequencing data. H3M2 outperforms GERMLINE and PLINK applied to the same training dataset, and most importantly it is less sensitive to parameter specification, ensuring that analysis results are not severely affected by the chosen parameter configuration as in GERMLINE and PLINK.
A standalone tool for working with annotated variant files, e.g. when searching for variants causing Mendelian disease. Very flexible in terms of input file formats, FILTUS offers efficient filtering and a range of downstream utilities, including statistical analysis of gene sharing patterns, detection of de novo mutations in trios, QC plots and autozygosity mapping. The autozygosity mapping is based on a hidden Markov model and enables accurate detection of autozygous regions directly from exome-scale variant files. FILTUS is primarily intended for WES-scale data, whole-genome data can be analysed by using the built-in prefiltering functionality.
Identifies homozygous stretches using new generation sequencing (NGS) data. HomSI was designed to define homozygous stretches in consanguineous families from NGS data. To identify and visualize the homozygous stretches, the software processes each variant and generates several graphs. It was evaluated using both a simulated dataset generated and a real dataset of three disease genes within the homozygous regions, which have been previously identified using a combination of exome and single-nucleotide polymorphism (SNP) microarray data.
Assists in calling runs of homozygosity in genotype data. GARLIC provides a model-based method for inferring runs of homozygosity (ROH) in genome-wide single nucleotide polymorphisms (SNPs) datasets. It works in four steps: (i) the window-based logarithm of the odds (LOD) score calculation, (ii) the kernel density estimation of LOD score distribution, (iii) the assembly of ROH, and (iv) gaussian mixture modeling of ROH size distribution.