Using bedtools with dbVar GVF and VCF ftp files
GVF and VCF formatted data for dbVar can be found in the dbVar FTP Manifest. Download the *.vcf.gz file or the corresponding *.gvf.gz file as needed.
Note: dbVar does not provide support for bedtools installation. Please follow the bedtools software provider installation instructions for your specific system.
Download gvf files from dbVar FTP:
|
https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/estd214.GRCh38.variant_region.gvf.gz https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd102.GRCh38.variant_region.gvf.gz |
Decompress files using gunzip:
|
gunzip estd214.GRCh38.variant_region.gvf.gz gunzip nstd102.GRCh38.variant_region.gvf.gz |
Command line example bedtools query:
| bedtools intersect -a estd214.GRCh38.variant_region.gvf -b nstd102.GRCh38.variant_region.gvf > estd214_nstd102_GRCh38.var.intersect.gvf |
On the command line use 'bedtools -h' for a complete list of bedtools sub-commands. Use 'bedtools sub-command -h' for Summary, Usage, Options, and notes on the bedtools sub-command.
Information on bedtools: http://bedtools.readthedocs.org/en/latest/
bedtools is also available on GitHub: https://github.com/arq5x/bedtools2