mutant interval identification

mutant interval identification

Community rating: ?????

From the mutant identification 1 pipeline (Workflow:Mutant Identification 1). A tool to take a SNP list input from a bulk segregant dataset (locations of mutant parent homozygous unique SNPs only) and determine the mutant phenotype inducing SNP interval based on allele frequency analysis (output as text file and pdf)-prioritizing blocks of conserved homozygosity with the parental dataset.

Quick Start

To use mutant interval identification, import your SNPs from bulk segregant dataset in text format-file formatted using the Workflow:Mutant Identification 1. Format (Chr \t Position \t Alternate allele \t %reads with alternate allele)
In addition a chromosome size file is needed an example file is: http://de.iplantcollaborative.org/dl/d/836C7CCE-DA89-4FF7-BE3A-2DFEC249F4D4/chrsizes_wheat.txt

Test Data

Test data for this app appears at:

Input File(s)

Use the 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.

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