Filter homozygous SNPs

Filter homozygous SNPs

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Takes SNP list input from; SNP calling illumina seq data Part2 using VarScan. If genome mapping reference is non-divergent use mutant parent SNP list here to format for Mutant Identification 1 pipeline using awk

Quick Start

Input File(s)

Use SNP file VarScan format 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 a text file named Final_mutant_specific_homozygotes.txt as output i.e. this will identify homozygous SNPs that are specific to the mutant parental line (SNPs from Workflow: SNP calling illumina seq data Part2).