Literature DB >> 25431635

Using SomaticSniper to Detect Somatic Single Nucleotide Variants.

David E Larson1, Travis E Abbott1, Richard K Wilson1.   

Abstract

Detecting somatic single nucleotide variants (SNVs) is an essential component of cancer research with next generation sequencing data. This protocol describes how to run the SomaticSniper somatic SNV detector and then filter the output to eliminate most false positives. It also includes support protocols detailing the compilation of the software.

Entities:  

Keywords:  next-generation sequencing; somatic variant calling; somaticsniper

Mesh：

Year:  2014        PMID： 25431635      PMCID： PMC4242521          DOI： 10.1002/0471250953.bi1505s45

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  10 in total

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

Authors:  Daniel C Koboldt; Qunyuan Zhang; David E Larson; Dong Shen; Michael D McLellan; Ling Lin; Christopher A Miller; Elaine R Mardis; Li Ding; Richard K Wilson
Journal:  Genome Res       Date:  2012-02-02       Impact factor: 9.043

2.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

3.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2011-09-08       Impact factor: 6.937

4.  SomaticSniper: identification of somatic point mutations in whole genome sequencing data.

Authors:  David E Larson; Christopher C Harris; Ken Chen; Daniel C Koboldt; Travis E Abbott; David J Dooling; Timothy J Ley; Elaine R Mardis; Richard K Wilson; Li Ding
Journal:  Bioinformatics       Date:  2011-12-06       Impact factor: 6.937

5.  A comprehensive catalogue of somatic mutations from a human cancer genome.

Authors:  Erin D Pleasance; R Keira Cheetham; Philip J Stephens; David J McBride; Sean J Humphray; Chris D Greenman; Ignacio Varela; Meng-Lay Lin; Gonzalo R Ordóñez; Graham R Bignell; Kai Ye; Julie Alipaz; Markus J Bauer; David Beare; Adam Butler; Richard J Carter; Lina Chen; Anthony J Cox; Sarah Edkins; Paula I Kokko-Gonzales; Niall A Gormley; Russell J Grocock; Christian D Haudenschild; Matthew M Hims; Terena James; Mingming Jia; Zoya Kingsbury; Catherine Leroy; John Marshall; Andrew Menzies; Laura J Mudie; Zemin Ning; Tom Royce; Ole B Schulz-Trieglaff; Anastassia Spiridou; Lucy A Stebbings; Lukasz Szajkowski; Jon Teague; David Williamson; Lynda Chin; Mark T Ross; Peter J Campbell; David R Bentley; P Andrew Futreal; Michael R Stratton
Journal:  Nature       Date:  2009-12-16       Impact factor: 49.962

6.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

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

Authors:  Christopher T Saunders; Wendy S W Wong; Sajani Swamy; Jennifer Becq; Lisa J Murray; R Keira Cheetham
Journal:  Bioinformatics       Date:  2012-05-10       Impact factor: 6.937

8.  An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data.

Authors:  Yuichi Shiraishi; Yusuke Sato; Kenichi Chiba; Yusuke Okuno; Yasunobu Nagata; Kenichi Yoshida; Norio Shiba; Yasuhide Hayashi; Haruki Kume; Yukio Homma; Masashi Sanada; Seishi Ogawa; Satoru Miyano
Journal:  Nucleic Acids Res       Date:  2013-03-06       Impact factor: 16.971

9.  Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.

Authors:  Alexis Christoforides; John D Carpten; Glen J Weiss; Michael J Demeure; Daniel D Von Hoff; David W Craig
Journal:  BMC Genomics       Date:  2013-05-04       Impact factor: 3.969

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

Authors:  Kristian Cibulskis; Michael S Lawrence; Scott L Carter; Andrey Sivachenko; David Jaffe; Carrie Sougnez; Stacey Gabriel; Matthew Meyerson; Eric S Lander; Gad Getz
Journal:  Nat Biotechnol       Date:  2013-02-10       Impact factor: 54.908
  10 in total

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