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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gbsTagsToSNP_TASSEL 3.0.133

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Aligns tags from the same physical location against one another, calls SNPs from each alignment, and then outputs the SNP genotypes to a HapMap format file (one file per chromosome).

Quick Start

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 -> gbs_workflow -> output.

Input File(s)

Use bwa_output.sam and myStudy.tbt.bin from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a folder of text files as output. For the test case, the output folder you will find in the example_data directory is named unfilt.

Tool Source for App

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