Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges

(2015) Biao Liu et al.   Oncotarget

The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations

(2014) M. Bodini et al.   BLOOD

Combining calls from multiple somatic mutation-callers

(2014) Su Kim et al.   BMC BIOINFORMATICS

Effective filtering strategies to improve data quality from population-based whole exome sequencing studies

(2014) Andrew R Carson et al.   BMC BIOINFORMATICS

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

(2014) Huilei Xu et al.   BMC GENOMICS

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

A comparative analysis of algorithms for somatic SNV detection in cancer

(2013) Nicola D. Roberts et al.   BIOINFORMATICS

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

(2013) Nancy F. Hansen et al.   BIOINFORMATICS

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

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

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

Performance of Common Analysis Methods for Detecting Low-Frequency Single Nucleotide Variants in Targeted Next-Generation Sequence Data

(2013) David H. Spencer et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

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

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

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

The transcriptional landscape and mutational profile of lung adenocarcinoma

(2012) J.-S. Seo et al.   GENOME RESEARCH

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

(2012) Gholson J Lyon et al.   Genome Medicine

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

(2011) Joke Reumers et al.   NATURE BIOTECHNOLOGY

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

Analysis of next-generation genomic data in cancer: accomplishments and challenges

(2010) L. Ding et al.   HUMAN MOLECULAR GENETICS

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS