Human Background Variation DataBase
hbvdb is a set of tools to handle the storage and exchange of genetic background frequencies.
It is specifically intended for genetic clinics and clinical genomics research groups, to catalogue variant frequencies in de-identified human exome or whole genome sequencing material.
The design allows the exclusion of particular phenotypes by simple tags, so that cases in one study can serve as controls in another, without violating personal integrity by storing complete genotypes. One can also add e.g. platform tags.
There are four components to this.
hbvdb-tools, an Open Source toolkit, for use in any environment supporting perl and VCFtools, including OS X and Linux. Written by Jessada Thutkawkorapin. Documentation, usage examples and tests can be found in the package. A new version with a stronger, easier to use data exchange support is being implemented.
Filtering ready variant tables and databases for download, for use in clinical research, with frequencies specific to the alleles we encounter in Swedish practice. By downloading you agree not to try to deidentify any samples, or to use the tag information in your own research without the consent of the contributing researchers.
|200 Danes||avdb|vcf|hbvdb [Li et al 2010]|
|249 Swedes||avdb|vcf|hbvdb [unpublished].|
A Standard Operating Procedure, broadly describing the procedure to include your samples in the database.
You and me, contributing data so that we can all benefit from more stable frequency estimates and good filtering for rare variants.
Clinical Genetics, Karolinska University Hospital
Department of Molecular Medicine and Surgery, Karolinska Institutet
Science for Life Laboratory, Stockholm