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dbVOR: A database system for importing pedigree, phenotype and genotype data and exporting selected subsets

Baron, RV and Conley, YP and Gorin, MB and Weeks, DE (2015) dbVOR: A database system for importing pedigree, phenotype and genotype data and exporting selected subsets. BMC Bioinformatics, 16 (1).

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Abstract

© 2015 Baron et al.; licensee BioMed Central. Background: When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources. Results: We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format. Conclusions: dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register . Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html .


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Baron, RVrvb5@pitt.eduRVB5
Conley, YPyconley@pitt.eduYCONLEY
Gorin, MB
Weeks, DEweeks@pitt.eduWEEKS0000-0001-9410-7228
Date: 12 December 2015
Date Type: Publication
Journal or Publication Title: BMC Bioinformatics
Volume: 16
Number: 1
DOI or Unique Handle: 10.1186/s12859-015-0505-4
Schools and Programs: Graduate School of Public Health > Biostatistics
Graduate School of Public Health > Human Genetics
School of Nursing > Nursing
Refereed: Yes
Date Deposited: 31 Aug 2016 16:09
Last Modified: 01 Nov 2017 14:06
URI: http://d-scholarship.pitt.edu/id/eprint/29389

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