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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.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> gbs_workflow -> output.
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.
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..