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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

To use population genomics analysis flow, import your data in bam/sam format.
Resources: http://creskolab.uoregon.edu/stacks/comp/ref_map.php

Test Data

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

http://creskolab.uoregon.edu/stacks/comp/ref_map.php