Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers
暂无分享,去创建一个
Jonas Behr | H. Moch | N. Beerenwinkel | P. Schraml | C. Beisel | J. Kuipers | Jochen Singer | A. L. Hofmann
[1] P. Humphrey,et al. The 2016 WHO Classification of Tumours of the Urinary System and Male Genital Organs-Part A: Renal, Penile, and Testicular Tumours. , 2016, European urology.
[2] Michael C. Heinold,et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing , 2015, Nature Communications.
[3] Ana Conesa,et al. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data , 2015, Bioinform..
[4] Andrew Menzies,et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing , 2015, Nature Medicine.
[5] J. Potash,et al. Validation and assessment of variant calling pipelines for next-generation sequencing , 2014, Human Genomics.
[6] D. Spandidos,et al. Emerging targeted therapies for melanoma treatment (Review) , 2014, International journal of oncology.
[7] Brandi L. Cantarel,et al. BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity , 2014, BMC Bioinformatics.
[8] Heng Li,et al. Toward better understanding of artifacts in variant calling from high-coverage samples , 2014, Bioinform..
[9] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[10] R. Satya,et al. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data , 2014, BMC Genomics.
[11] P. A. Futreal,et al. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing , 2014, Nature Genetics.
[12] Benjamin J. Raphael,et al. Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine , 2014, Genome Medicine.
[13] Peilin Jia,et al. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers , 2013, Genome Medicine.
[14] Mauricio O. Carneiro,et al. From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.
[15] Xiaoqing Yu,et al. Comparing a few SNP calling algorithms using low-coverage sequencing data , 2013, BMC Bioinformatics.
[16] R. Daniel Kortschak,et al. A comparative analysis of algorithms for somatic SNV detection in cancer , 2013, Bioinform..
[17] Vineet Bafna,et al. Wessim: a whole-exome sequencing simulator based on in silico exome capture , 2013, Bioinform..
[18] I. Cuesta,et al. Comparison of variant calling methods in exome sequencing of matched tumor-normal sample pairs , 2013 .
[19] H. Hakonarson,et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing , 2013, Genome Medicine.
[20] A. Sivachenko,et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.
[21] Michael R. Speicher,et al. A survey of tools for variant analysis of next-generation genome sequencing data , 2013, Briefings Bioinform..
[22] Gabor T. Marth,et al. Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.
[23] T. Takano,et al. Olaparib in platinum-sensitive ovarian cancer. , 2012, The New England journal of medicine.
[24] K. Polyak,et al. Intra-tumour heterogeneity: a looking glass for cancer? , 2012, Nature Reviews Cancer.
[25] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[26] Christopher A. Miller,et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.
[27] Ken Chen,et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data , 2012, Bioinform..
[28] Sohrab P. Shah,et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data , 2012, Bioinform..
[29] M. Gerstung,et al. Reliable detection of subclonal single-nucleotide variants in tumour cell populations , 2012, Nature Communications.
[30] Tatiana Popova,et al. Supplementary Methods , 2012, Acta Neuropsychiatrica.
[31] Gholamreza Haffari,et al. Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data , 2011, Bioinform..
[32] Heng Li,et al. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..
[33] Kristian Cibulskis,et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data , 2011, Bioinform..
[34] Denis C. Bauer. Variant calling comparison CASAVA1.8 and GATK , 2011 .
[35] M. DePristo,et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.
[36] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[37] Thomas Seufferlein,et al. Targeted treatments in colorectal cancer: state of the art and future perspectives , 2010, Gut.
[38] Emily H Turner,et al. Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.
[39] R. Elston,et al. Choosing an optimal method to combine P‐values , 2009, Statistics in medicine.
[40] Knut Reinert,et al. SeqAn An efficient, generic C++ library for sequence analysis , 2008, BMC Bioinformatics.
[41] S. Gabriel,et al. EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy , 2004, Science.
[42] Faraz Hach,et al. SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA , 2017, Bioinform..
[43] Francesco Vallania,et al. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. , 2014, The Journal of molecular diagnostics : JMD.
[44] T. Speed,et al. Comparing somatic mutation-callers: beyond Venn diagrams , 2013, BMC Bioinformatics.
[45] Ira M. Hall,et al. BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..
[46] Claude-Alain H. Roten,et al. Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..
[47] S. Kunte. Statistical computing , 2000 .