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Items: 1 to 20 of 445

1.

Variant callers for next-generation sequencing data: a comparison study.

Liu X, Han S, Wang Z, Gelernter J, Yang BZ.

PLoS One. 2013 Sep 27;8(9):e75619. doi: 10.1371/journal.pone.0075619. eCollection 2013.

2.

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.

3.

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.

4.

Challenges in exome analysis by LifeScope and its alternative computational pipelines.

Pranckevičiene E, Rančelis T, Pranculis A, Kučinskas V.

BMC Res Notes. 2015 Sep 7;8:421. doi: 10.1186/s13104-015-1385-4.

5.

Validation and assessment of variant calling pipelines for next-generation sequencing.

Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, McCombie WR, Zandi PP.

Hum Genomics. 2014 Jul 30;8:14. doi: 10.1186/1479-7364-8-14.

6.

VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering.

Gézsi A, Bolgár B, Marx P, Sarkozy P, Szalai C, Antal P.

BMC Genomics. 2015 Oct 28;16:875. doi: 10.1186/s12864-015-2050-y.

7.

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.

Laurie S, Fernandez-Callejo M, Marco-Sola S, Trotta JR, Camps J, Chacón A, Espinosa A, Gut M, Gut I, Heath S, Beltran S.

Hum Mutat. 2016 Dec;37(12):1263-1271. doi: 10.1002/humu.23114. Epub 2016 Sep 26.

8.

Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken.

Ni G, Strom TM, Pausch H, Reimer C, Preisinger R, Simianer H, Erbe M.

BMC Genomics. 2015 Oct 21;16:824. doi: 10.1186/s12864-015-2059-2.

9.

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers.

Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H, Beerenwinkel N.

BMC Bioinformatics. 2017 Jan 3;18(1):8. doi: 10.1186/s12859-016-1417-7.

10.

A study on fast calling variants from next-generation sequencing data using decision tree.

Li Z, Wang Y, Wang F.

BMC Bioinformatics. 2018 Apr 19;19(1):145. doi: 10.1186/s12859-018-2147-9.

11.

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.

12.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.

Bizon C, Spiegel M, Chasse SA, Gizer IR, Li Y, Malc EP, Mieczkowski PA, Sailsbery JK, Wang X, Ehlers CL, Wilhelmsen KC.

BMC Genomics. 2014 Jan 30;15:85. doi: 10.1186/1471-2164-15-85.

13.

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

O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ.

Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013.

14.

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.

Trubetskoy V, Rodriguez A, Dave U, Campbell N, Crawford EL, Cook EH, Sutcliffe JS, Foster I, Madduri R, Cox NJ, Davis LK.

Bioinformatics. 2015 Jan 15;31(2):187-93. doi: 10.1093/bioinformatics/btu591. Epub 2014 Sep 29.

15.

Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance.

Kumar P, Al-Shafai M, Al Muftah WA, Chalhoub N, Elsaid MF, Aleem AA, Suhre K.

BMC Res Notes. 2014 Oct 22;7:747. doi: 10.1186/1756-0500-7-747.

16.

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference.

Cornish A, Guda C.

Biomed Res Int. 2015;2015:456479. doi: 10.1155/2015/456479. Epub 2015 Oct 11.

17.

Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data.

Kumaran M, Subramanian U, Devarajan B.

BMC Bioinformatics. 2019 Jun 17;20(1):342. doi: 10.1186/s12859-019-2928-9.

18.

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.

19.

Comparing a few SNP calling algorithms using low-coverage sequencing data.

Yu X, Sun S.

BMC Bioinformatics. 2013 Sep 17;14:274. doi: 10.1186/1471-2105-14-274.

20.

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals.

Cheng AY, Teo YY, Ong RT.

Bioinformatics. 2014 Jun 15;30(12):1707-13. doi: 10.1093/bioinformatics/btu067. Epub 2014 Feb 19.

PMID:
24558117

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