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 2 AntEpiSeeker Conversion

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This application converts transposed PLINK (.tfam/.tped) to the proper input format for AntEpiSeeker 2.0.

Limitations

  1. The phenotypes must be binary traits, e.g. cancer or health.
  2. The genotypes MUST be heterozygous with only two heritability traits.

Quick Start

  • Input file format transposed PLINK (.tfam/.tped)
  • Enter the output file BASE name

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under _Community Data -> iplantcollaborative -> example_data -> antepiseekerconversion

Input File(s)

If you have one of the alternative PLINK formats, (.map/.ped, .bed/.bim/.fam), then use PLINK Conversion to convert to transposed PLINK file format (.tfam/.tped).  Then use PLINK 2 AntEpiSeeker Conversion to convert transposed PLINK file format (.tfam/.tped) to the proper AntEpiSeeker input format for the Genotype File.  If you have an alternative file format that is not PLINK, then use Tassel3 Conversion or Tassel4 Conversion to attain the standard PLINK file format (.map/.ped), then follow the above directions.

Output File(s)

Expect two output files, one of which is error.txt, which will contain some errors if the script was unable to run.  The second one will be *.ant depending on what you input as the BASE file name.  The *.ant file is the proper Genotype input file for AntEpiSeeker 2.0.

Tool Source for App

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