1 - 8 of 8 results

VarScan

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.

deepSNV

Provides quantitative variant callers for detecting subclonal mutations in ultra-deep sequencing experiments. DeepSNV is a comparative targeted deep-sequencing approach combined with a customised statistical algorithm, which can detect and quantify subclonal single-nucleotide variants (SNVs) in mixed populations. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and the shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters.

Strelka

Provides analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Strelka is a variant calling method building upon the innovative Strelka somatic variant caller to improve upon aspects of variant calling for both germline and somatic analysis. The germline caller employs an efficient tiered haplotype model to improve accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. The germline caller also analyzes input sequencing data using a mixture-model indel error estimation method to improve robustness to indel noise.

LoFreq

A sensitive and robust approach for calling single-nucleotide variants (SNVs) from high-coverage sequencing datasets, based on a formal model for biases in sequencing error rates. LoFreq adapts automatically to sequencing run and position-specific sequencing biases and can call SNVs at a frequency lower than the average sequencing error rate in a dataset. LoFreq’s robustness, sensitivity and specificity were validated using several simulated and real datasets (viral, bacterial and human) and on two experimental platforms (Fluidigm and Sequenom).

SiNVICT

A computational method that detects single nucleotide variants (SNVs) and short indels from circulating cell-free DNA (cfDNA) sequencing data. SiNVICT increases the sensitivity and specificity of SNV and indel detection at very low variant allele frequencies. It has the capability to handle multiple sequencing platforms with different error properties; it minimises false positives resulting from mapping errors and other technology specific artifacts including strand bias and low base quality at read ends. SiNVICT also has the capability to perform time-series analysis, where samples from a patient sequenced at multiple time points are jointly examined to report locations of interest where there is a possibility that certain clones were wiped out by some treatment while some subclones gained selective advantage. We compared SiNVICT with other popular SNV callers such as MuTect, VarScan2, and Freebayes. Our results show that SiNVICT performs better than these tools in most cases and allows further data exploration such as time-series analysis on cfDNA sequencing data.

OutLyzer

Includes two main operating modes: (1) a classical variant-caller; (2) a tool to evaluate local quality metrics. OutLyzer estimates the sum of several background noise sources, including sequencing mistakes, errors generated by sample preparation and bioinformatics analysis, based on an outlier detection algorithm. For a given sample, this tool evaluates whether a mutation is present at a given position, specifies all raw sequencing information and assesses local background noise.