MAC: identifying and correcting annotation for multi-nucleotide variations

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Novel multi-nucleotide polymorphisms in the human genome characterized by whole genome and exome sequencing

(2010) Jeffrey A. Rosenfeld et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

TP53mutation signature supports involvement of aristolochic acid in the aetiology of endemic nephropathy-associated tumours

(2008) Tatiana Nedelko et al.   INTERNATIONAL JOURNAL OF CANCER