Published August 3, 2020
| Version v1
Dataset
Open
GREEN-VARAN SV annotation resources
Authors/Creators
- 1. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Description
This dataset contains a collection of BED files prepared to be used with the SV_annotation tool, part of GREEN-VARAN.
GREEN-DB regions
Regulatory regions collected in GREEN-DB (see https://github.com/edg1983/GREEN-VARAN)
Population AF annotations
These files represent SVs from gnomAD v.2.1.1, 1000G phase3, and the IMH dataset. When not directly available, the GRCh38 versions are obtained by coordinates liftover from GRCh37.
If you use AF annotations don't forget to cite also the original papers:
- gnomAD paper as described in https://gnomad.broadinstitute.org/terms
- 1000G SV paper: https://www.nature.com/articles/nature15394
- the original IMH publication https://www.nature.com/articles/s41586-020-2371-0
Gene annotations
Genes and CDSs annotations are from GENCODE v33 basic set
Files
Files
(278.5 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:5e10fd436c13db9a747eeaa9a687f92a
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278.5 MB | Download |
Additional details
Related works
- Is derived from
- Dataset: https://storage.googleapis.com/gnomad-public/papers/2019-sv/gnomad_v2.1_sv.sites.vcf.gz (URL)
- Dataset: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz (URL)
- Dataset: https://github.com/hall-lab/sv_paper_042020/blob/master/Supplementary_File_1.zip (URL)
- Dataset: https://github.com/hall-lab/sv_paper_042020/blob/master/Supplementary_File_2.zip (URL)