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Items: 1 to 20 of 114

1.

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M.

Nat Biotechnol. 2014 Mar;32(3):246-51. doi: 10.1038/nbt.2835. Epub 2014 Feb 16.

PMID:
24531798
2.

svclassify: a method to establish benchmark structural variant calls.

Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M.

BMC Genomics. 2016 Jan 16;17:64. doi: 10.1186/s12864-016-2366-2.

3.

ReliableGenome: annotation of genomic regions with high/low variant calling concordance.

Popitsch N; WGS500 Consortium, Schuh A, Taylor JC.

Bioinformatics. 2017 Jan 15;33(2):155-160. doi: 10.1093/bioinformatics/btw587. Epub 2016 Sep 7.

4.

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.

Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL, Kruglyak S, Margulies EH, McVean G, Bentley DR.

Genome Res. 2017 Jan;27(1):157-164. doi: 10.1101/gr.210500.116. Epub 2016 Nov 30.

5.

Toward better understanding of artifacts in variant calling from high-coverage samples.

Li H.

Bioinformatics. 2014 Oct 15;30(20):2843-51. doi: 10.1093/bioinformatics/btu356. Epub 2014 Jun 27. Review.

6.

An analytical workflow for accurate variant discovery in highly divergent regions.

Tian S, Yan H, Neuhauser C, Slager SL.

BMC Genomics. 2016 Sep 2;17:703. doi: 10.1186/s12864-016-3045-z.

7.

Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.

8.

Medical implications of technical accuracy in genome sequencing.

Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT, Salit M, Ashley EA.

Genome Med. 2016 Mar 2;8(1):24. doi: 10.1186/s13073-016-0269-0.

9.

Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery.

Chan EY.

Methods Mol Biol. 2009;578:95-111. doi: 10.1007/978-1-60327-411-1_5.

PMID:
19768588
10.

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data.

Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA; CAAPA Consortium.

Bioinformatics. 2017 Apr 15;33(8):1147-1153. doi: 10.1093/bioinformatics/btw786.

11.

Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.

Greminger MP, Stölting KN, Nater A, Goossens B, Arora N, Bruggmann R, Patrignani A, Nussberger B, Sharma R, Kraus RH, Ambu LN, Singleton I, Chikhi L, van Schaik CP, Krützen M.

BMC Genomics. 2014 Jan 10;15:16. doi: 10.1186/1471-2164-15-16.

12.

Comparison of solution-based exome capture methods for next generation sequencing.

Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J.

Genome Biol. 2011 Sep 28;12(9):R94. doi: 10.1186/gb-2011-12-9-r94.

13.

INDELseek: detection of complex insertions and deletions from next-generation sequencing data.

Au CH, Leung AY, Kwong A, Chan TL, Ma ES.

BMC Genomics. 2017 Jan 5;18(1):16. doi: 10.1186/s12864-016-3449-9.

14.

A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data.

Krishnan SG, Waters DL, Henry RJ.

Methods Mol Biol. 2014;1099:287-94. doi: 10.1007/978-1-62703-715-0_24.

PMID:
24243213
15.

Performance evaluation of indel calling tools using real short-read data.

Hasan MS, Wu X, Zhang L.

Hum Genomics. 2015 Aug 19;9:20. doi: 10.1186/s40246-015-0042-2.

16.

Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.

Kim RN, Kim DS, Choi SH, Yoon BH, Kang A, Nam SH, Kim DW, Kim JJ, Ha JH, Toyoda A, Fujiyama A, Kim A, Kim MY, Park KH, Lee KS, Park HS.

DNA Res. 2012 Jun;19(3):275-87. doi: 10.1093/dnares/dss011. Epub 2012 Apr 3.

17.

Systematic comparison of variant calling pipelines using gold standard personal exome variants.

Hwang S, Kim E, Lee I, Marcotte EM.

Sci Rep. 2015 Dec 7;5:17875. doi: 10.1038/srep17875.

18.

Identification of indels in next-generation sequencing data.

Ratan A, Olson TL, Loughran TP Jr, Miller W.

BMC Bioinformatics. 2015 Feb 13;16:42. doi: 10.1186/s12859-015-0483-6.

19.

Impact of post-alignment processing in variant discovery from whole exome data.

Tian S, Yan H, Kalmbach M, Slager SL.

BMC Bioinformatics. 2016 Oct 3;17(1):403.

20.

A probabilistic approach for SNP discovery in high-throughput human resequencing data.

Hoberman R, Dias J, Ge B, Harmsen E, Mayhew M, Verlaan DJ, Kwan T, Dewar K, Blanchette M, Pastinen T.

Genome Res. 2009 Sep;19(9):1542-52. doi: 10.1101/gr.092072.109. Epub 2009 Jul 15.

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