SNP calling illumina seq data Part 2

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Last updated: Oct 10, 2014 by lgardineVersion comment
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SNP calling illumina seq data Part 2

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Requires BAM file output from; Mapping illumina seq data Part1, and filters un-mapped and non-uniquely mapped reads from this mapping analysis to call SNPs using VarScan. SNPs used as input for; Identification of unique homozygous SNPs in mutant

Quick Start

  • To use SNP calling illumina seq data Part 2, import your data in BAM format.
  • Current setup for diploid organisms

Test Data

Test data for this app appears directly in the link: http://de.iplantcollaborative.org/dl/d/58DA9AAF-597F-4BE3-B9F4-ECFA19B583F4/bwa_output.sorted.21668.bam

Input File(s)

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.

Output File(s)

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

Tool Source for App