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Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers.

Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, Dahlman KB, Pao W, Zhao Z.

Genome Med. 2013 Oct 11;5(10):91. doi: 10.1186/gm495. eCollection 2013.


Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.

Krøigård AB, Thomassen M, Lænkholm AV, Kruse TA, Larsen MJ.

PLoS One. 2016 Mar 22;11(3):e0151664. doi: 10.1371/journal.pone.0151664. eCollection 2016.


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.


In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data.

Cai L, Yuan W, Zhang Z, He L, Chou KC.

Sci Rep. 2016 Nov 22;6:36540. doi: 10.1038/srep36540.


A comparative analysis of algorithms for somatic SNV detection in cancer.

Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL.

Bioinformatics. 2013 Sep 15;29(18):2223-30. doi: 10.1093/bioinformatics/btt375. Epub 2013 Jul 9.


Comparison of somatic mutation calling methods in amplicon and whole exome sequence data.

Xu H, DiCarlo J, Satya RV, Peng Q, Wang Y.

BMC Genomics. 2014 Mar 28;15:244. doi: 10.1186/1471-2164-15-244.


Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.

do Valle ÍF, Giampieri E, Simonetti G, Padella A, Manfrini M, Ferrari A, Papayannidis C, Zironi I, Garonzi M, Bernardi S, Delledonne M, Martinelli G, Remondini D, Castellani G.

BMC Bioinformatics. 2016 Nov 8;17(Suppl 12):341. doi: 10.1186/s12859-016-1190-7.


Practicability of detecting somatic point mutation from RNA high throughput sequencing data.

Sheng Q, Zhao S, Li CI, Shyr Y, Guo Y.

Genomics. 2016 May;107(5):163-9. doi: 10.1016/j.ygeno.2016.03.006. Epub 2016 Apr 2.


SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.

Kockan C, Hach F, Sarrafi I, Bell RH, McConeghy B, Beja K, Haegert A, Wyatt AW, Volik SV, Chi KN, Collins CC, Sahinalp SC.

Bioinformatics. 2017 Jan 1;33(1):26-34. doi: 10.1093/bioinformatics/btw536. Epub 2016 Aug 16.


Detailed comparison of two popular variant calling packages for exome and targeted exon studies.

Warden CD, Adamson AW, Neuhausen SL, Wu X.

PeerJ. 2014 Sep 30;2:e600. doi: 10.7717/peerj.600. eCollection 2014.


Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.

Sandmann S, de Graaf AO, Karimi M, van der Reijden BA, Hellström-Lindberg E, Jansen JH, Dugas M.

Sci Rep. 2017 Feb 24;7:43169. doi: 10.1038/srep43169.


Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection.

Koboldt DC, Larson DE, Wilson RK.

Curr Protoc Bioinformatics. 2013 Dec;44:15.4.1-17. doi: 10.1002/0471250953.bi1504s44.


Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.

Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G.

Nat Biotechnol. 2013 Mar;31(3):213-9. doi: 10.1038/nbt.2514. Epub 2013 Feb 10.


Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution.

Stead LF, Sutton KM, Taylor GR, Quirke P, Rabbitts P.

Hum Mutat. 2013 Oct;34(10):1432-8. doi: 10.1002/humu.22365. Epub 2013 Jul 11.


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.


VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK.

Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. Epub 2012 Feb 2.


A three-caller pipeline for variant analysis of cancer whole-exome sequencing data.

Liu ZK, Shang YK, Chen ZN, Bian H.

Mol Med Rep. 2017 May;15(5):2489-2494. doi: 10.3892/mmr.2017.6336. Epub 2017 Mar 16.


Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.

Stubbs A, McClellan EA, Horsman S, Hiltemann SD, Palli I, Nouwens S, Koning AH, Hoogland F, Reumers J, Heijsman D, Swagemakers S, Kremer A, Meijerink J, Lambrechts D, van der Spek PJ.

J Clin Bioinforma. 2012 Nov 19;2(1):19. doi: 10.1186/2043-9113-2-19.


Evaluation of variant detection software for pooled next-generation sequence data.

Huang HW; NISC Comparative Sequencing Program, Mullikin JC, Hansen NF.

BMC Bioinformatics. 2015 Jul 29;16:235. doi: 10.1186/s12859-015-0624-y.


Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK.

Bioinformatics. 2012 Jul 15;28(14):1811-7. doi: 10.1093/bioinformatics/bts271. Epub 2012 May 10.


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