A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: 1) germline variants (SNPs and indels) in individual samples or pools of samples, 2) multi-sample variants (shared or private) in multi-sample datasets (with mpileup), 3) somatic mutations, LOH events, and germline variants in tumor-normal pairs and 4) somatic copy number alterations (CNAs) in tumor-normal exome data.
Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and able to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
A software tool for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation discovery in exome analysis and fragment information to identify the parental origin of germ-line mutations.
A computational tool for calculating probability of variants in family-based sequencing data. It is still challenging to call rare variants. In family-based sequencing studies, information from all family members should be utilized to more accurately identify new germline mutations. FamSeq serves this purpose by providing the probability of an individual carrying a variant given his/her entire family’s raw measurements. FamSeq accommodates de novo mutations and can perform variant calling at chrX.
A reliable big data-based computational toolset for efficiently manipulating genome-wide variants, annotations and every-site coverage in NGS studies. SeqHBase uses a heuristic framework of inheritance information for detecting de novo, inherited homozygous or compound heterozygous mutations that may be disease-contributing in trios, nuclear families and/or extended families. It shows very good performance on three different examples of family based sequencing data and is scalable by virtue of its basis on MapReduce framework.
Implements a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing (NGS) data. Polymutt simplifies detection and genotyping of single nucleotide polymorphisms (SNPs). It aims to facilitate the study of families, rare variants and de novo mutation events. It also intends to transform sequence data into accurate genotypes.
Consists of a linkage-disequilibrium framework to genotype inference in parents-offspring trios. TrioCaller implements a method to call genotypes and infer haplotypes for whole genome shotgun sequencing data collected in trios, unrelated individuals, or parent-offspring pairs. The software can facilitate genotype calling and haplotype inference for sequencing projects.