Community rating: ?????
Aligns tags from the same physical location against one another, calls SNPs from each alignment, and then outputs the SNP genotypes to a HapMap format file (one file per chromosome).
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 bwa_output.sam and myStudy.tbt.bin from the directory above as test input.
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 unfilt.