BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

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

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Exome sequencing generates high quality data in non-target regions

(2012) Yan Guo et al.   BMC GENOMICS

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

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

(2011) Matthew N Bainbridge et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS