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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gbsFilter_TASSEL 3.0.133

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Reads HapMap format genotype files (one per chromosome) and filters out SNPs with low taxon coverage (missing data at most taxa), high heterozygosity, low (and/or high) minor allele frequency, or that are not in LD with at least one neighboring SNP.

Quick Start

Test Data


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 folder mergedSNPs 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 filt..

Tool Source for App

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