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Items: 1 to 20 of 125

1.

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.

Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JS, Ridge PG.

BMC Bioinformatics. 2014;15 Suppl 7:S12. doi: 10.1186/1471-2105-15-S7-S12. Epub 2014 May 28.

2.

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.

3.

VCF-kit: assorted utilities for the variant call format.

Cook DE, Andersen EC.

Bioinformatics. 2017 May 15;33(10):1581-1582. doi: 10.1093/bioinformatics/btx011.

4.

vcfr: a package to manipulate and visualize variant call format data in R.

Knaus BJ, Grünwald NJ.

Mol Ecol Resour. 2017 Jan;17(1):44-53. doi: 10.1111/1755-0998.12549. Epub 2016 Jul 12.

PMID:
27401132
5.

Isomorphic semantic mapping of variant call format (VCF2RDF).

Penha ED, Iriabho E, Dussaq A, de Oliveira DM, Almeida JS.

Bioinformatics. 2017 Feb 15;33(4):547-548. doi: 10.1093/bioinformatics/btw652.

6.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

7.

Canary: an atomic pipeline for clinical amplicon assays.

Doig KD, Ellul J, Fellowes A, Thompson ER, Ryland G, Blombery P, Papenfuss AT, Fox SB.

BMC Bioinformatics. 2017 Dec 15;18(1):555. doi: 10.1186/s12859-017-1950-z.

8.

FMFilter: A fast model based variant filtering tool.

Akgün M, Faruk Gerdan Ö, Görmez Z, Demirci H.

J Biomed Inform. 2016 Apr;60:319-27. doi: 10.1016/j.jbi.2016.02.013. Epub 2016 Feb 27.

9.

Unified representation of genetic variants.

Tan A, Abecasis GR, Kang HM.

Bioinformatics. 2015 Jul 1;31(13):2202-4. doi: 10.1093/bioinformatics/btv112. Epub 2015 Feb 19.

10.

Improved VCF normalization for accurate VCF comparison.

Bayat A, Gaëta B, Ignjatovic A, Parameswaran S.

Bioinformatics. 2017 Apr 1;33(7):964-970. doi: 10.1093/bioinformatics/btw748.

PMID:
27993787
11.

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.

Zhang C, Dong SS, Xu JY, He WM, Yang TL.

Bioinformatics. 2018 Oct 15. doi: 10.1093/bioinformatics/bty875. [Epub ahead of print]

PMID:
30321304
12.

VCF-Explorer: filtering and analysing whole genome VCF files.

Akgün M, Demirci H.

Bioinformatics. 2017 Nov 1;33(21):3468-3470. doi: 10.1093/bioinformatics/btx422.

PMID:
29036499
13.

cyvcf2: fast, flexible variant analysis with Python.

Pedersen BS, Quinlan AR.

Bioinformatics. 2017 Jun 15;33(12):1867-1869. doi: 10.1093/bioinformatics/btx057.

14.

High-Throughput Tabular Data Processor - Platform independent graphical tool for processing large data sets.

Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, Messiaen LM, Piotrowski A.

PLoS One. 2018 Feb 12;13(2):e0192858. doi: 10.1371/journal.pone.0192858. eCollection 2018.

15.

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.

Preston MD, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo JB, Nosten F, Anderson T, Clark TG.

Bioinformatics. 2012 Nov 15;28(22):2983-5. doi: 10.1093/bioinformatics/bts557. Epub 2012 Sep 13.

16.

myVCF: a desktop application for high-throughput mutations data management.

Pietrelli A, Valenti L.

Bioinformatics. 2017 Nov 15;33(22):3676-3678. doi: 10.1093/bioinformatics/btx475.

PMID:
29036298
17.

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.

18.

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.

Lee S, Lee S, Ouellette S, Park WY, Lee EA, Park PJ.

Nucleic Acids Res. 2017 Jun 20;45(11):e103. doi: 10.1093/nar/gkx193.

19.

DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research.

Pandey RV, Pabinger S, Kriegner A, Weinhäusel A.

Hum Mutat. 2017 Jul;38(7):778-787. doi: 10.1002/humu.23227. Epub 2017 May 30.

PMID:
28397319
20.

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

Katta MA, Khan AW, Doddamani D, Thudi M, Varshney RK.

PLoS One. 2015 Oct 13;10(10):e0139868. doi: 10.1371/journal.pone.0139868. eCollection 2015.

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