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VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.

Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8. doi: 10.1093/nar/gks572. Epub 2012 Jun 11.


Snat: a SNP annotation tool for bovine by integrating various sources of genomic information.

Jiang J, Jiang L, Zhou B, Fu W, Liu JF, Zhang Q.

BMC Genet. 2011 Oct 7;12:85. doi: 10.1186/1471-2156-12-85.


WEP: a high-performance analysis pipeline for whole-exome data.

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.

BMC Bioinformatics. 2013;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.


SNVerGUI: a desktop tool for variant analysis of next-generation sequencing data.

Wang W, Hu W, Hou F, Hu P, Wei Z.

J Med Genet. 2012 Dec;49(12):753-5. doi: 10.1136/jmedgenet-2012-101001. Epub 2012 Sep 28.


VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era.

Cheng YC, Hsiao FC, Yeh EC, Lin WJ, Tang CY, Tseng HC, Wu HT, Liu CK, Chen CC, Chen YT, Yao A.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W76-81. doi: 10.1093/nar/gks397. Epub 2012 May 22.


NGS catalog: A database of next generation sequencing studies in humans.

Xia J, Wang Q, Jia P, Wang B, Pao W, Zhao Z.

Hum Mutat. 2012 Jun;33(6):E2341-55. doi: 10.1002/humu.22096. Epub 2012 Apr 19.


GrabBlur--a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files.

Stade B, Seelow D, Thomsen I, Krawczak M, Franke A.

BMC Genomics. 2014;15 Suppl 4:S8. doi: 10.1186/1471-2164-15-S4-S8. Epub 2014 May 20.


SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics.

Lechat P, Souche E, Moszer I.

BMC Bioinformatics. 2013 Sep 22;14:277. doi: 10.1186/1471-2105-14-277.


Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.

Reumers J, Conde L, Medina I, Maurer-Stroh S, Van Durme J, Dopazo J, Rousseau F, Schymkowitz J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D825-9. Epub 2007 Dec 17.


PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis.

Freimuth RR, Stormo GD, McLeod HL.

Hum Mutat. 2005 Feb;25(2):110-7.


The human FOXL2 mutation database.

Beysen D, Vandesompele J, Messiaen L, De Paepe A, De Baere E.

Hum Mutat. 2004 Sep;24(3):189-93.

12. a web application for interpreting human variations.

Ou M, Ma R, Cheung J, Lo K, Yee P, Luo T, Chan TL, Au CH, Kwong A, Luo R, Lam TW.

Bioinformatics. 2015 Dec 15;31(24):4035-7. doi: 10.1093/bioinformatics/btv500. Epub 2015 Aug 26.


A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.


Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.

San Lucas FA, Wang G, Scheet P, Peng B.

Bioinformatics. 2012 Feb 1;28(3):421-2. doi: 10.1093/bioinformatics/btr667. Epub 2011 Dec 2.


MutDB services: interactive structural analysis of mutation data.

Dantzer J, Moad C, Heiland R, Mooney S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W311-4.


Identification of causal sequence variants of disease in the next generation sequencing era.

Kingsley CB.

Methods Mol Biol. 2011;700:37-46. doi: 10.1007/978-1-61737-954-3_3. Review.


VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants.

Ho ED, Cao Q, Lee SD, Yip KY.

BMC Genomics. 2014 Oct 11;15:886. doi: 10.1186/1471-2164-15-886.


PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data.

Zhang L, Zhang J, Yang J, Ying D, Lau YL, Yang W.

Bioinformatics. 2013 Jan 1;29(1):124-5. doi: 10.1093/bioinformatics/bts627. Epub 2012 Oct 25.


SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing.

Spinella JF, Mehanna P, Vidal R, Saillour V, Cassart P, Richer C, Ouimet M, Healy J, Sinnett D.

BMC Genomics. 2016 Nov 14;17(1):912.


VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.

Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP.

Brief Bioinform. 2016 Mar;17(2):346-51. doi: 10.1093/bib/bbv051. Epub 2015 Jul 25.

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