The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Plink Conversion

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This application converts all the PLINK file formats (ped/map, tped/tfam, or bed/bim/fam) to other PLINK file formats.

Quick Start

  • Select ONE of the following filesets: Regular, Transposed or Binary.
  • Input ALL of the required files in that fileset.
  • Select the wanted Output File Format.
  • Enter a new output file BASE name, if desired.  A BASE name is the name without the extension.
  • Resources: http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#recode

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> PlinkConversion.

Input File(s)

There three possible input formats, only one may be used at a time.   Make sure to follow the directions on the application when entering input data.  For example, if using the regular fileset (.map/.ped) then enter the inputs into .map and .ped box respectively, leaving all other input boxes empty.  If using transposed fileset (.tfam/.tped) then enter inputs in the labeled .tfam and .tped boxes, leaving the other boxes empty .  In ADDITION the user must go to the parameters section and check the box saying 'Transposed files are inputs'.  The same thing must be done when entering the binary fileset.

  1. Regular Fileset (.map/.ped).
  2. Transposed Fileset (.tfam/.tped)
  3. Binary Fileset (.bed/.bim/.fam)

Output File(s)

There are ten different kinds of output possible, depending on the selection that is made, and only one of the options can be chosen.  Once again all formats are variations of PLINK format, and can be referenced from the Input File(s) section. 

  1. Regular Fileset (.map/.ped)
  2. Transposed Fileset (.tfam/.tped)
  3. Binary Fileset (.bed/.bim/.fam)
  4. Long-format Fileset (.lgen/.map/.fam)
  5. Raw-format w/ additive coding (.raw) [Required input for Random Jungle]
  6. Raw-format w/ additive/dominance codine (.raw)[Required input for Random Jungle]
  7. The Regular fileset (.map/.ped) with 1/2 allele coding
  8. Fastphase file format
  9. Bimbam file format
  10. Structure file format

Expect a number of text files with the output file BASE name as output, with the proper extensions, depending on the choice that was made.  In addition to the ones expected there may be various other output files created.

Tool Source for App

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