VarScan-2.3.6 SNP caller
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variant detection in massively parallel sequencing data.
- To use VarScan-2.3.6 SNP caller, import your data in pileup format.
- Resources: http://varscan.sourceforge.net/using-varscan.html
Use the linked file 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 SNP file as output. For the test case, the output file you will find at the link: http://de.iplantcollaborative.org/dl/d/D9756156-1FA1-48D5-83A3-77F49F2A4829/RIL71.snp