Variant Calling

Data Processing and Germline Variant Calling with the Sentieon pipeline.- MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling.- Octopus: Genotyping and Haplotyping in Diverse Experimental Designs.- Accurate Ensemble Prediction of Somatic Mutations with SMuRF2.- Detecting Medium and Large Insertions and Deletions with Transindel.- DECoN: A detection and visualisation tool for exonic copy number variants.- FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing.- Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms.- Structural Variant Detection from Long-Read Sequencing Data with cuteSV.- Identifying Somatic Mitochondrial DNA Mutations.- Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq data using SplAdder.- PipeIT: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data.- Variant calling from RNA-seq data using the GATK joint genotyping workflow.- UMI-Varcal: a low-frequency variant caller for UMI-tagged paired-end sequencing data .- Alignment-free genotyping of known variations with MALVA.- Kmer2SNP: Reference-free heterozygous SNP calling using k-mer frequency distributions.- Somatic Single Nucleotide Variant Calling from Single Cell DNA sequencing data using SCAN-SNV.- Copy Number Variation Detection by Single-Cell DNA sequencing with SCOPE.- Variant Annotation and Functional Prediction: SnpEff.- Annotating Cancer-Related Variants At Protein-Protein Interface with Structure-PPi.- Preanalytical Variables and Sample Quality Control For Clinical Variant Analysis.