ToTem: a tool for variant calling pipeline optimization

Low-burden TP53 mutations in chronic phase of myeloproliferative neoplasms: association with age, hydroxyurea administration, disease type and JAK2 mutational status

(2017) B Kubesova et al.   LEUKEMIA

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

(2017) Sarah Sandmann et al.   Scientific Reports

ReliableGenome: annotation of genomic regions with high/low variant calling concordance

(2016) Niko Popitsch et al.   BIOINFORMATICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Medical implications of technical accuracy in genome sequencing

(2016) Rachel L. Goldfeder et al.   Genome Medicine

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

(2015) Sohyun Hwang et al.   Scientific Reports

SM a SH: a benchmarking toolkit for human genome variant calling

(2014) Ameet Talwalkar et al.   BIOINFORMATICS

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Subclonal variant calling with multiple samples and prior knowledge

(2014) M. Gerstung et al.   BIOINFORMATICS

Detailed analysis of therapy-driven clonal evolution of TP53 mutations in chronic lymphocytic leukemia

(2014) J Malcikova et al.   LEUKEMIA

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Next-generation sequencing in the clinic

(2013) Jason Y Park et al.   NATURE BIOTECHNOLOGY

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

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

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

(2011) Mark A DePristo et al.   NATURE GENETICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS