Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

Clonal expansion and linear genome evolution through breast cancer progression from pre-invasive stages to asynchronous metastasis

(2015) Anne Bruun Krøigård et al.   Oncotarget

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Combining calls from multiple somatic mutation-callers

(2014) Su Kim et al.   BMC BIOINFORMATICS

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data

(2014) Huilei Xu et al.   BMC GENOMICS

A comparative analysis of algorithms for somatic SNV detection in cancer

(2013) Nicola D. Roberts et al.   BIOINFORMATICS

Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes

(2013) Mamunur Rashid et al.   BIOINFORMATICS

Shimmer: detection of genetic alterations in tumors using next-generation sequence data

(2013) Nancy F. Hansen et al.   BIOINFORMATICS

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

(2013) Alexis Christoforides et al.   BMC GENOMICS

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data

(2013) Yuichi Shiraishi et al.   NUCLEIC ACIDS RESEARCH

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Virmid: accurate detection of somatic mutations with sample impurity inference

(2013) Sangwoo Kim et al.   GENOME BIOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH