Resource 533

Name:

Automating gene data download

This scripts assists in downloading bulk genome information by looping through all the chromosomes for a particular file type. It takes a single parameter specifying the Field ID of the data to acquire. The Application specific authentication file ".ukbkey" must also be present in the current directory.

Examples:

• "gene_multi.sh 22418" will download all genotype calls information,
• "gene_multi.sh 22438" will download all haplotype information,

Before runing the script change the extension from ".txt" to ".sh" and do "chmod 700" to make it executable. Note that it will produce some harmless error messages for the imputed "higher" chromosomes and exome data which does not exist.

This resource can be downloaded or viewed using the link: gene_multi.txt

If you have wget available (typically on linux systems), then you can also obtain a copy using the command

 wget  -nd  biobank.ctsu.ox.ac.uk/ukb/ukb/misc/gene_multi.txt