MyVCF: A desktop application for high-throughput mutations data management

Alessandro Pietrelli, Luca Valenti

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Summary Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the â 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants. We developed myVCF, a standalone, easy-to-use desktop application, which is based on a browser interface and is suitable for Windows, Mac and UNIX systems. myVCF is an efficient platform that is able to manage multiple sequencing projects created from VCF files within the system; stores genetic variants and samples genotypes from an annotated VCF files into a SQLite database; implements a flexible search engine for data exploration, allowing to query for chromosomal region, gene, single variant or dbSNP ID. Besides, myVCF generates a summary statistics report about mutations distribution across samples and across the genome/exome by aggregating the information within the VCF file. In summary, the myVCF platform allows end-users without strong programming and bioinformatics skills to explore, query, visualize and export mutations data in a simple and straightforward way. Availability and implementation https://apietrelli.github.io/myVCF/ Contact pietrelli@ingm.org Supplementary informationSupplementary dataare available at Bioinformatics online.

Original languageEnglish
Pages (from-to)3676-3678
Number of pages3
JournalBioinformatics
Volume33
Issue number22
DOIs
Publication statusPublished - Nov 15 2017

Fingerprint

Bioinformatics
Data Management
Computational Biology
Information management
High Throughput
Mutation
Genes
Throughput
Sequencing
Exome
Search Engine
UNIX
Search engines
Genotype
Research Personnel
Statistics
Availability
Genome
Databases
Query

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

MyVCF : A desktop application for high-throughput mutations data management. / Pietrelli, Alessandro; Valenti, Luca.

In: Bioinformatics, Vol. 33, No. 22, 15.11.2017, p. 3676-3678.

Research output: Contribution to journalArticle

Pietrelli, Alessandro ; Valenti, Luca. / MyVCF : A desktop application for high-throughput mutations data management. In: Bioinformatics. 2017 ; Vol. 33, No. 22. pp. 3676-3678.
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