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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Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.

population genomics analysis flow

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software to perform population genomics analysis using samples for which reference genomes exist. Program can accept SAM/BAM files. Calculates Fst, Fis, and expected/observed heterzygosity

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 -> stacks demo-> population_genomics

Input File(s)

Use all .sam samples 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 described in the next section below.

Output File(s)

Expect csv files named after the input files as output and some batch files containing all the data for all samples.

Tool Source for App

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