Variant recalibration software tools | Whole-genome sequencing data analysis
Accurate genomic variant detection is an essential step in gleaning medically useful information from genome data. However, low concordance among variant-calling methods reduces confidence in the clinical validity of whole genome and exome sequence data, and confounds downstream analysis for applications in genome medicine.
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.
Calculates concordant and discordant regions with respect to a set of surveyed variant calling (VC) pipelines. ReliableGenome combines call sets derived by multiple pipelines from arbitrary numbers of datasets and interpolates expected concordance for genomic regions without data. Our method can be applied to arbitrary VC pipelines and the resulting genomic partitions can be used for variant filtering, annotation and prioritization or for focusing computational resources on hard-to-analyse regions of the genome.
Automatically integrates variant calling pipelines into an overall model that predicts accurate variant probabilities. VariantMetaCaller utilizes support vector machines (SVM) to merge multiple information sources built by variant calling pipelines. It can be used to determine probabilities of variants. This tool can produce probabilistic scores for calls even in areas, such as in targeted gene panels or organisms.
Filters candidate variants according to the given criteria. FMFilter can handle compound heterozygous and de novo models properly. It offers options to make filtering according to genotype quality, read depth, gene name, mutation type and custom annotated population frequency. This tool can find out compound heterozygous mutations. It provides an alternative for the analysis of next-generation sequencing data collected by Mendelian's disease research.
Provides a method for combining sets of SNP variant calls produced by different variant calling programs. The integrated set of SNP variant calls produced by BAYSIC™ improves the sensitivity and specificity of the variant calls used as input. In addition to combining sets of germline variants, BAYSIC can also be used to combine sets of somatic mutations detected in the context of tumor/normal sequencing experiments.