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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construction genetic map

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This tool will accept aligned samples in BAM/Bowtie format in order to build loci ready to be used for the construction of a genetic map.

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 ->stacks demo-> genetic_map.

Input File(s)

Use male.sam as a male parent input file female.sam as a female parent input file and as progeny the rest of the .sam files from the directory above as test input.

Parameters Used in App

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

Output File(s)

Expect as output csv files named after the input files as output. There will be some files called batch files, they contain the genotypes for all individuals for analysis.

Tool Source for App

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