EAGLE: Explicit Alternative Genome Likelihood Evaluator

On genomic repeats and reproducibility

(2016) Can Firtina et al.   BIOINFORMATICS

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

(2016) Anne Bruun Krøigård et al.   PLoS One

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

(2015) Goo Jun et al.   GENOME RESEARCH

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

(2013) S. B. Montgomery et al.   GENOME RESEARCH

Calreticulin gene exon 9 frameshift mutations in patients with thrombocytosis

(2013) J Chi et al.   LEUKEMIA

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

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

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

Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia

(2012) Eric J Duncavage et al.   MODERN PATHOLOGY

A mostly traditional approach improves alignment of bisulfite-converted DNA

(2012) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

(2011) Daniel F Simola et al.   GENOME BIOLOGY

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

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