Jul 27, 2015

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

Briefings in Bioinformatics
Steven N HartJean-Pierre A Kocher

Abstract

Next-generation sequencing platforms are widely used to discover variants associated with disease. The processing of sequencing data involves read alignment, variant calling, variant annotation and variant filtering. The standard file format to hold variant calls is the variant call format (VCF) file. According to the format specifications, any arbitrary annotation can be added to the VCF file for downstream processing. However, most downstream analysis programs disregard annotations already present in the VCF and re-annotate variants using the annotation provided by that particular program. This precludes investigators who have collected information on variants from literature or other sources from including these annotations in the filtering and mining of variants. We have developed VCF-Miner, a graphical user interface-based stand-alone tool, to mine variants and annotation stored in the VCF. Powered by a MongoDB database engine, VCF-Miner enables the stepwise trimming of non-relevant variants. The grouping feature implemented in VCF-Miner can be used to identify somatic variants by contrasting variants in tumor and in normal samples or to identify recessive/dominant variants in family studies. It is not limited to human dat...Continue Reading

Mentioned in this Paper

Study
Research
Genetic Analysis
Institution
CISD2
Neoplasms
Nucleic Acid Sequencing
Shprintzen Syndrome
Bikinia le-testui
Computer Programs and Programming

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