The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Mutant Identification 1

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Takes mutant parent specific homozygous SNPs from; Workflow:Identification of unique homozygous SNPs in mutant OR App: Filter homozygous SNPs. Also takes bulk segregant mutant sample SNP list from; SNP calling illumina seq data Part2. Locates parental homozygous SNP locations in the bulk segregant data. Performs mutant interval identification prioritizing blocks of conserved homozygosity in the bulk segregant data.

Quick Start

  • To use Mutant Identification 1, import your data in SNP list VarScan format (bulk segregant mutant sample raw SNPs) and mutant parent specific homozygous SNPs.

Test Data

Input File(s)

Use the files above as test input. Plus a file of chromosome sizes.

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.

Output File(s)

Expect 2 files as output. For a test case, the output pdf file is: http://de.iplantcollaborative.org/dl/d/06B2D49D-F898-46E3-9B1E-45C5CB5F33E0/Output.pdf and the output text file is: http://de.iplantcollaborative.org/dl/d/AF93039F-F7AE-406D-8828-50FC776D4256/Output

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