General
This package installs the UK Biobank file handler binaries and encoding file, which can be manually sourced from https://biobank.ndph.ox.ac.uk/showcase/download.cgi. The UK Biobank binaries are installed to /usr/bin/, while the encoding.dat file is installed to /var/lib/ukbprep/encoding/.
Detailed documentation on the use of the binaries contained within this package can be found in the Accessing UKB Data guide.
ukbmd5, ukbunpack & ukbconv - Core Binaries
ukbunpack & ukbconv are the binaries that most people will require to unpack and convert their UK Biobank data to a usable form. I have included ukbmd5 for completeness, even though its functionality can be entirely replicated by the md5sum command.
ukbmd5- Calculate size and MD5 of a fileukbunpack- Unpack (decrypt and decompress) UKB dataukbconv- Convert unpacked UKB data to other formatsdconvert- Convert unpacked data to other formats
The various options ukbconv accepts can be viewed by executing ukbconv (without any arguments) in the terminal. To use the bundled encoding.ukb file, simply provide the local path of the encoding.dat file to ukbconv using the -e flag, e.g.
ukbconv [input_file] [format] -e /var/lib/ukbprep/encoding/encoding.dat
Alternatively, the 'encoding file' (optionally required by ukbconv) can by found at UK Biobank Data Showcase download 301.
Detailed usage instructions for ukbmd5, ukbunpack & ukbconv can be found in sections 2.4--2.6 of the Accessing UKB Data guide.
ukbfetch - Accessing Bulk Data within UK Biobank
The various options ukbfetch accepts can be viewed by executing ukbfetch (without any arguments) in the terminal.
Detailed usage instructions can be found at UK Biobank Data Showcase resource 644 and in section 3.2 of the Accessing UKB Data guide.
gfetch - Accessing Genetic Data within UK Biobank
The various options gfetch accepts can be viewed by executing gfetch (without any arguments) in the terminal. Note, I have also included a ukbgfetch alias for gfetch.
Detailed usage instructions can be found at UK Biobank Data Showcase resource 668 and in section 4.2 of the Accessing UKB Data guide.
ukblink - Accessing Returned Data within UK Biobank
The various options ukblink accepts can be viewed by executing ukblink (without any arguments) in the terminal.
Detailed usage instructions can be found at UK Biobank Data Showcase resource 655 and in section 6.2 of the Accessing UKB Data guide.
Pinned Comments
Feakster commented on 2020-12-19 10:53 (UTC) (edited on 2023-05-24 09:55 (UTC) by Feakster)
General
This package installs the UK Biobank file handler binaries and encoding file, which can be manually sourced from https://biobank.ndph.ox.ac.uk/showcase/download.cgi. The UK Biobank binaries are installed to
/usr/bin/, while the encoding.dat file is installed to/var/lib/ukbprep/encoding/.Detailed documentation on the use of the binaries contained within this package can be found in the Accessing UKB Data guide.
ukbmd5,ukbunpack&ukbconv- Core Binariesukbunpack&ukbconvare the binaries that most people will require to unpack and convert their UK Biobank data to a usable form. I have includedukbmd5for completeness, even though its functionality can be entirely replicated by themd5sumcommand.ukbmd5- Calculate size and MD5 of a fileukbunpack- Unpack (decrypt and decompress) UKB dataukbconv- Convert unpacked UKB data to other formatsdconvert- Convert unpacked data to other formatsThe various options
ukbconvaccepts can be viewed by executingukbconv(without any arguments) in the terminal. To use the bundled encoding.ukb file, simply provide the local path of the encoding.dat file toukbconvusing the-eflag, e.g.Alternatively, the 'encoding file' (optionally required by
ukbconv) can by found at UK Biobank Data Showcase download 301.Detailed usage instructions for
ukbmd5,ukbunpack&ukbconvcan be found in sections 2.4--2.6 of the Accessing UKB Data guide.ukbfetch- Accessing Bulk Data within UK BiobankThe various options
ukbfetchaccepts can be viewed by executingukbfetch(without any arguments) in the terminal.Detailed usage instructions can be found at UK Biobank Data Showcase resource 644 and in section 3.2 of the Accessing UKB Data guide.
gfetch- Accessing Genetic Data within UK BiobankThe various options
gfetchaccepts can be viewed by executinggfetch(without any arguments) in the terminal. Note, I have also included aukbgfetchalias forgfetch.Detailed usage instructions can be found at UK Biobank Data Showcase resource 668 and in section 4.2 of the Accessing UKB Data guide.
ukblink- Accessing Returned Data within UK BiobankThe various options
ukblinkaccepts can be viewed by executingukblink(without any arguments) in the terminal.Detailed usage instructions can be found at UK Biobank Data Showcase resource 655 and in section 6.2 of the Accessing UKB Data guide.