population genomics analysis flow
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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.