varcmp.bib

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@article{Langmead:2012fk,
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@article{Li:2013aa,
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@article{Paten:2014aa,
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	Journal = {arXiv:1404.5010},
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	Year = {2014}}

@article{Narzisi:2014aa,
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	title = {Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly},
	year = {2014},
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	journal = {bioRxiv}
}

@article{Talwalkar:2013aa,
	Author = {Ameet Talwalkar and others},
	Journal = {arXiv:1310.8420},
	Title = {{SMaSH}: A Benchmarking Toolkit for Human Genome Variant Calling},
	Year = {2013}}

@article{Li:2009uq,
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	Journal = {Bioinformatics},
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@article{Depristo:2011vn,
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	Journal = {Nat Genet},
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@article{Li:2011ab,
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	Journal = {Bioinformatics},
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@article{1000g:2012aa,
	Author = {{1000 Genomes Project Consortium}},
	Journal = {Nature},
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	Title = {An integrated map of genetic variation from 1,092 human genomes},
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@article{Garrison:2012aa,
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	Journal = {arXiv:1207.3907},
	Title = {Haplotype-based variant detection from short-read sequencing},
	Year = {2012}}

@article{Olshen:2004aa,
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@article{Gymrek:2012aa,
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	Journal = {Genome Res},
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@article{Conrad:2011kx,
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	Journal = {Nat Genet},
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	Year = {2011}}

@article{Li:2012fk,
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	Journal = {Bioinformatics},
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	Title = {Exploring single-sample {SNP} and {INDEL} calling with whole-genome de novo assembly},
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	Year = {2012}}

@article{Zerbino:2008uq,
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	Journal = {Genome Res},
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	Title = {Velvet: algorithms for de novo short read assembly using {de Bruijn} graphs},
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	Year = {2008}}

@article{Levy:2007uq,
	Author = {Levy, Samuel and others},
	Journal = {PLoS Biol},
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	Title = {The diploid genome sequence of an individual human},
	Volume = {5},
	Year = {2007}}

@article{Bentley:2008cr,
	Author = {Bentley, David R and others},
	Journal = {Nature},
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	Title = {Accurate whole human genome sequencing using reversible terminator chemistry},
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	Year = {2008}}

@article{Wang:2008nx,
	Author = {Wang, Jun and others},
	Journal = {Nature},
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@article{Watson:2013aa,
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	Journal = {Nat Rev Genet},
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	Title = {Emerging patterns of somatic mutations in cancer},
	Volume = {14},
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@article{Campbell:2013aa,
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	Journal = {Trends Genet},
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@article{Li:2011ij,
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	Journal = {Nature},
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@article{Bamshad:2011aa,
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	Journal = {Nat Rev Genet},
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	Title = {Exome sequencing as a tool for {Mendelian} disease gene discovery},
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@article{Zook:2014aa,
	Author = {Zook, Justin M and others},
	Journal = {Nat Biotechnol},
	Title = {Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls},
	Year = {2014}}

@article{Harismendy:2009aa,
	Author = {Harismendy, Olivier and others},
	Journal = {Genome Biol},
	Pages = {R32},
	Title = {Evaluation of next generation sequencing platforms for population targeted sequencing studies},
	Volume = {10},
	Year = {2009}}

@article{Lam:2012aa,
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	Journal = {Nat Biotechnol},
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@article{Boland:2013aa,
	Author = {Boland, Joseph F and others},
	Journal = {Hum Genet},
	Pages = {1153-63},
	Title = {The new sequencer on the block: comparison of {Life Technology}'s {Proton} sequencer to an {Illumina} {HiSeq} for whole-exome sequencing},
	Volume = {132},
	Year = {2013}}

@article{Clark:2011aa,
	Author = {Clark, Michael J and others},
	Journal = {Nat Biotechnol},
	Pages = {908-14},
	Title = {Performance comparison of exome {DNA} sequencing technologies},
	Volume = {29},
	Year = {2011}}

@article{Lam:2012fk,
	Author = {Lam, Hugo Y K and others},
	Journal = {Nat Biotechnol},
	Pages = {78-82},
	Title = {Performance comparison of whole-genome sequencing platforms},
	Volume = {30},
	Year = {2012}}

@article{Loman:2012aa,
	Author = {Loman, Nicholas J and others},
	Journal = {Nat Biotechnol},
	Pages = {434-9},
	Title = {Performance comparison of benchtop high-throughput sequencing platforms},
	Volume = {30},
	Year = {2012}}

@article{Nickles:2012aa,
	Author = {Nickles, Dorothee and others},
	Journal = {BMC Genomics},
	Pages = {477},
	Title = {In depth comparison of an individual's {DNA} and its lymphoblastoid cell line using whole genome sequencing},
	Volume = {13},
	Year = {2012}}

@article{ORawe:2013aa,
	Author = {O'Rawe, Jason and others},
	Journal = {Genome Med},
	Pages = {28},
	Title = {Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing},
	Volume = {5},
	Year = {2013}}

@article{Veltman:2012aa,
	Author = {Veltman, Joris A and Brunner, Han G},
	Journal = {Nat Rev Genet},
	Pages = {565-75},
	Title = {De novo mutations in human genetic disease},
	Volume = {13},
	Year = {2012}}

@article{Liu:2013aa,
	Author = {Liu, Xiangtao and others},
	Journal = {PLoS One},
	Pages = {e75619},
	Title = {Variant callers for next-generation sequencing data: a comparison study},
	Volume = {8},
	Year = {2013}}

@article{Li:2008zr,
	Author = {Li, Heng and others},
	Journal = {Genome Res},
	Pages = {1851-8},
	Title = {Mapping short {DNA} sequencing reads and calling variants using mapping quality scores},
	Volume = {18},
	Year = {2008}}

@article{Li:2010kx,
	Author = {Li, Heng and others},
	Journal = {Brief Bioinform},
	Pages = {473-83},
	Title = {A survey of sequence alignment algorithms for next-generation sequencing},
	Volume = {11},
	Year = {2010}}

@article{Bolosky:2014aa,
	Author = {William J. Bolosky and others},
	Journal = {Unpublished},
	Title = {{SNAP}: fast, accurate sequence alignment enabling biological applications},
	Year = {2014}}

@article{Li:2013ab,
	Author = {Li, Shengting and others},
	Journal = {Genome Res},
	Pages = {195-200},
	Title = {{SOAPindel}: efficient identification of indels from short paired reads},
	Volume = {23},
	Year = {2013}}

@article{Li:2011ac,
	Author = {Li, Mingyao and others},
	Journal = {Science},
	Pages = {53-8},
	Title = {Widespread {RNA} and {DNA} sequence differences in the human transcriptome},
	Volume = {333},
	Year = {2011}}

@article{Pickrell:2012aa,
	Author = {Pickrell, Joseph K and others},
	Journal = {Science},
	Pages = {1302},
	Title = {Comment on ``Widespread {RNA} and {DNA} sequence differences in the human transcriptome''},
	Volume = {335},
	Year = {2012}}

@article{Lin:2012aa,
	Author = {Lin, Wei and others},
	Journal = {Science},
	Pages = {1302; author reply 1302},
	Title = {Comment on ``Widespread {RNA} and {DNA} sequence differences in the human transcriptome''},
	Volume = {335},
	Year = {2012}}

@article{Kleinman:2012aa,
	Author = {Kleinman, Claudia L and Majewski, Jacek},
	Journal = {Science},
	Pages = {1302; author reply 1302},
	Title = {Comment on ``Widespread {RNA} and {DNA} sequence differences in the human transcriptome''},
	Volume = {335},
	Year = {2012}}

@article{Larson:2012aa,
	Author = {Larson, David E and others},
	Journal = {Bioinformatics},
	Pages = {311-7},
	Title = {{SomaticSniper}: identification of somatic point mutations in whole genome sequencing data},
	Volume = {28},
	Year = {2012}}

@article{Lower:2012aa,
	Author = {L{\"o}wer, Martin and others},
	Journal = {PLoS Comput Biol},
	Pages = {e1002714},
	Title = {Confidence-based somatic mutation evaluation and prioritization},
	Volume = {8},
	Year = {2012}}

@article{Goode:2013aa,
	Author = {Goode, David L and others},
	Journal = {Genome Med},
	Pages = {90},
	Title = {A simple consensus approach improves somatic mutation prediction accuracy},
	Volume = {5},
	Year = {2013}}

@article{Roberts:2013aa,
	Author = {Roberts, Nicola D and others},
	Journal = {Bioinformatics},
	Pages = {2223-30},
	Title = {A comparative analysis of algorithms for somatic SNV detection in cancer},
	Volume = {29},
	Year = {2013}}

@article{Kim:2013aa,
	Author = {Kim, Su Yeon and Speed, Terence P},
	Journal = {BMC Bioinformatics},
	Pages = {189},
	Title = {Comparing somatic mutation-callers: beyond {Venn} diagrams},
	Volume = {14},
	Year = {2013}}

@article{Robasky:2014aa,
	Author = {Robasky, Kimberly and others},
	Journal = {Nat Rev Genet},
	Pages = {56-62},
	Title = {The role of replicates for error mitigation in next-generation sequencing},
	Volume = {15},
	Year = {2014}}

@article{Li:2011kx,
	Author = {Li, Heng},
	Journal = {Bioinformatics},
	Pages = {1157-8},
	Title = {Improving {SNP} discovery by base alignment quality},
	Volume = {27},
	Year = {2011}}

@article{Albers:2011aa,
	Author = {Albers, Cornelis A and others},
	Journal = {Genome Res},
	Pages = {961-73},
	Title = {Dindel: accurate indel calls from short-read data},
	Volume = {21},
	Year = {2011}}

@article{Homer:2010aa,
	Author = {Homer, Nils and Nelson, Stanley F},
	Journal = {Genome Biol},
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	Title = {Improved variant discovery through local re-alignment of short-read next-generation sequencing data using {SRMA}},
	Volume = {11},
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@article{DBLP:journals/corr/abs-1010-2656,
	Author = {Jouni Sir{\'e}n and others},
	Journal = {CoRR},
	Title = {Indexing Finite Language Representation of Population Genotypes},
	Volume = {abs/1010.2656},
	Year = {2010}}

@article{Cheng:2014aa,
	Author = {Cheng, Anthony Youzhi and others},
	Journal = {Bioinformatics},
	Month = {Feb},
	Title = {Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals},
	Year = {2014}}

@article{Nakamura:2011aa,
	Author = {Nakamura, Kensuke and others},
	Journal = {Nucleic Acids Res},
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	Pages = {e90},
	Title = {Sequence-specific error profile of Illumina sequencers},
	Volume = {39},
	Year = {2011}}