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  1. Method: Calling amplified haplotypes in next generation tumor sequence data
    • Ninad Dewal,
    • Yang Hu,
    • Matthew L. Freedman,
    • Thomas LaFramboise,
    • and Itsik Pe'er
    Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
    .... This was performed previously on SNP arrays at the single SNP level (Dewal et al. 2010; LaFramboise et al. 2010) and can now be extended to next generation sequencing data. HATS' reporting of the amplified allele may serve as a first step in this downstream analysis possibility. One benefit is that sites that were...
  2. Resource: Benchmarking small-variant genotyping in polyploids
    • Daniel P. Cooke,
    • David C. Wedge,
    • and Gerton Lunter
    Genome Res. February 2022 32: 403-408; Published in Advance December 29, 2021, doi:10.1101/gr.275579.121
    ....1101/201178 ↵Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, et al. 2018. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 36: 983–987. doi:10.1038/nbt.4235 ↵Potato Genome Sequencing Consortium. 2011. Genome sequence...
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  3. Method: Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Yann Surget-Groba and
    • Juan I. Montoya-Burgos
    Genome Res. October 2010 20: 1432-1440; Published in Advance August 6, 2010, doi:10.1101/gr.103846.109
    ...(Montoya-Burgos et al. 2010), the detection of new alternative splice variants (Carninci 2008; Gibbons et al. 2009; Tang et al. 2009), allele-specific gene expression (Main et al. 2009), SNP discovery in genes (Barbazuk et al. 2007), or epigenetic gene regulation (Elling and Deng 2009). These advances...
  4. Resource: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • Aaron McKenna,
    • Matthew Hanna,
    • Eric Banks,
    • Andrey Sivachenko,
    • Kristian Cibulskis,
    • Andrew Kernytsky,
    • Kiran Garimella,
    • David Altshuler,
    • Stacey Gabriel,
    • Mark Daly,
    • and Mark A. DePristo
    Genome Res. September 2010 20: 1297-1303; Published in Advance July 19, 2010, doi:10.1101/gr.107524.110
    ..., Wold B, Mortazavi A. 2009. Computation for ChIP-seq and RNAseq studies. Nat Methods 6: S22–S32. Shendure J, Ji H. 2008. Next-generation DNA sequencing.Nat Biotechnol 26: 1135–1145. Sherry S, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski E, Sirotkin K. 2001. dbSNP: The NCBI database of genetic...
  5. Methods: A probabilistic approach for SNP discovery in high-throughput human resequencing data
    • Rose Hoberman,
    • Joana Dias,
    • Bing Ge,
    • Eef Harmsen,
    • Michael Mayhew,
    • Dominique J. Verlaan,
    • Tony Kwan,
    • Ken Dewar,
    • Mathieu Blanchette,
    • and Tomi Pastinen
    Genome Res. September 2009 19: 1542-1552; Published in Advance July 15, 2009, doi:10.1101/gr.092072.109
    ...A probabilistic approach for SNP discovery in high-throughput human resequencing data Rose Hoberman 1 , 2 , Joana Dias 3 , Bing Ge 3 , Eef Harmsen 3 , Michael Mayhew 1 , 2 , Dominique J. Verlaan 3 , 4 , 5 , Tony Kwan 3...
  6. Research: Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network
    • Nicolas Chassaing,
    • Erica E. Davis,
    • Kelly L. McKnight,
    • Adrienne R. Niederriter,
    • Alexandre Causse,
    • Véronique David,
    • Annaïck Desmaison,
    • Sophie Lamarre,
    • Catherine Vincent-Delorme,
    • Laurent Pasquier,
    • Christine Coubes,
    • Didier Lacombe,
    • Massimiliano Rossi,
    • Jean-Louis Dufier,
    • Helene Dollfus,
    • Josseline Kaplan,
    • Nicholas Katsanis,
    • Heather C. Etchevers,
    • Stanislas Faguer,
    • and Patrick Calvas
    Genome Res. April 2016 26: 474-485; Published in Advance February 18, 2016, doi:10.1101/gr.196048.115
    ...filtering that focused exclusively on alleles that were (1) absent from dbSNP132 (http://www.ncbi.nlm.nih.gov/projects/ SNP/; Sherry et al. 2001), HapMap (http://hapmap.ncbi.nlm.nih. gov/; The International HapMap 3 Consortium et al. 2010), 1000 Genomes (http://www.1000s.org/; The 1000 Genomes Project...
  7. Resource: SNP detection for massively parallel whole-genome resequencing
    • Ruiqiang Li,
    • Yingrui Li,
    • Xiaodong Fang,
    • Huanming Yang,
    • Jian Wang,
    • Karsten Kristiansen,
    • and Jun Wang
    Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108
    ...technology. One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole- or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed...
  8. Methods: Overlapping pools for high-throughput targeted resequencing
    • Snehit Prabhu and
    • Itsik Pe'er
    Genome Res. July 2009 19: 1254-1261; Published in Advance May 15, 2009, doi:10.1101/gr.088559.108
    ...MAQ (Li et al. 2008), and SNPs were called on the alignment. Since available algorithms call alleles under the assumption that they are looking at reads from a single individual (allele frequency 0, 1, or 2), we built our own SNP-calling algorithm for pooled data (refer Supplemental Methods...
  9. Research: Discovery and genotyping of structural variation from long-read haploid genome sequence data
    • John Huddleston,
    • Mark J.P. Chaisson,
    • Karyn Meltz Steinberg,
    • Wes Warren,
    • Kendra Hoekzema,
    • David Gordon,
    • Tina A. Graves-Lindsay,
    • Katherine M. Munson,
    • Zev N. Kronenberg,
    • Laura Vives,
    • Paul Peluso,
    • Matthew Boitano,
    • Chen-Shin Chin,
    • Jonas Korlach,
    • Richard K. Wilson,
    • and Evan E. Eichler
    Genome Res. May 2017 27: 677-685; Published in Advance November 28, 2016, doi:10.1101/gr.214007.116
    ...-deletion variants identified in 179 human s. Genome Res 23: 749–761. ↵Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308–311. ↵Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, et al...
  10. Method: Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
    • Filipe G. Vieira,
    • Matteo Fumagalli,
    • Anders Albrechtsen,
    • and Rasmus Nielsen
    Genome Res. November 2013 23: 1852-1861; Published in Advance August 15, 2013, doi:10.1101/gr.157388.113
    .... Molecular signatures of natural selection. Annu Rev Genet 39: 197–218. Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12: 443–451. Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J. 2012. SNP calling, genotype calling...
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