UkbiobankDump

Dump data https://afb.ukbiobank.ac.uk/ ukbiobank server. The server might not like too many requests. Use a your own risk. Doesn't work with jdk17 (?!)

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar ukbbdump  [options] Files

Usage: ukbbdump [options] Files
  Options:
    --api
      API base url
      Default: https://afb.ukbiobank.ac.uk/api
    --debug
      debug
      Default: false
  * -R, --dict
      A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --region
      limit to that region. An interval as the following syntax : 
      "chrom:start-end". Some jvarkit programs also allow the following syntax 
      : "chrom:middle+extend"  or "chrom:start-end+extend" or 
      "chrom:start-end+extend-percent%".A program might use a Reference 
      sequence to fix the chromosome name (e.g: 1->chr1)
    --retry
      max-retry
      Default: 10
    --seconds
      wait 'x' seconds between each call to the API
      Default: 10
    --version
      print version and exit
    -o
      Output file. Optional . Default: stdout

Keywords

• ukbiobank

Creation Date

20250425

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/ukbiobank/UkbiobankDump.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite ukbbdump ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

WARNING

I cannot explain why this software doesn't run with jdk17 (I always get a http error 403) but runs with jdk23...

$ java -jar jvarkit.jar ukbbdump -R ref.dict --region "chr3:38000000-39000000" 
Chrom   Pos rsID    Ref Alt nHomozygotes    HGVSp   maxImpact   maxConsequence  alleleCount alleleNum   alleleFreq  geneSymbol
chr3    38000013    .   A   G   0   NM_001370264.1:c.672+574A>G,NM_001370265.1:c.573+574A>G,NM_001385038.1:c.1182+574A>G,NM_001385039.1:c.1182+574A>G,NM_015873.4:c.1182+574A>G LOWEST  intron_variant  13  981062  0.0000132509464233657   VILL
chr3    38000014    .   G   A   0   NM_001370264.1:c.672+575G>A,NM_001370265.1:c.573+575G>A,NM_001385038.1:c.1182+575G>A,NM_001385039.1:c.1182+575G>A,NM_015873.4:c.1182+575G>A LOWEST  intron_variant  3   981092  0.0000030578172077644096    VILL
chr3    38000015    .   G   A   0   NM_001370264.1:c.672+576G>A,NM_001370265.1:c.573+576G>A,NM_001385038.1:c.1182+576G>A,NM_001385039.1:c.1182+576G>A,NM_015873.4:c.1182+576G>A LOWEST  intron_variant  3   981092  0.0000030578172077644096    VILL
chr3    38000018    rs1319217247    G   A   0   NM_001370264.1:c.672+579G>A,NM_001370265.1:c.573+579G>A,NM_001385038.1:c.1182+579G>A,NM_001385039.1:c.1182+579G>A,NM_015873.4:c.1182+579G>A LOWEST  intron_variant  2   981088  0.0000020385531165400047    VILL
chr3    38000021    rs6806791   G   A   32  NM_001370264.1:c.672+582G>A,NM_001370265.1:c.573+582G>A,NM_001385038.1:c.1182+582G>A,NM_001385039.1:c.1182+582G>A,NM_015873.4:c.1182+582G>A LOWEST  intron_variant  1342    981080  0.0013678802951848984   VILL
chr3    38000022    rs937502348 T   C   0   NM_001370264.1:c.672+583T>C,NM_001370265.1:c.573+583T>C,NM_001385038.1:c.1182+583T>C,NM_001385039.1:c.1182+583T>C,NM_015873.4:c.1182+583T>C LOWEST  intron_variant  4   981070  0.0000040771810370309966    VILL
chr3    38000027    .   T   C   0   NM_001370264.1:c.672+588T>C,NM_001370265.1:c.573+588T>C,NM_001385038.1:c.1182+588T>C,NM_001385039.1:c.1182+588T>C,NM_015873.4:c.1182+588T>C LOWEST  intron_variant  1   981072  0.0000010192931813363342    VILL
chr3    38000033    .   C   G   0   NM_001370264.1:c.672+594C>G,NM_001370265.1:c.573+594C>G,NM_001385038.1:c.1182+594C>G,NM_001385039.1:c.1182+594C>G,NM_015873.4:c.1182+594C>G LOWEST  intron_variant  3   981056  0.000003057929414834627 VILL