Mercurial > repos > richjp > cloudmap_zebrafish_hom_mapping

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author richjp
date Mon, 13 Oct 2014 08:42:19 -0400
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<?xml version="1.0"?>
<tool_dependency>
    <package name="ghostscript" version="9.10">
        <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="graphicsmagick" version="1.3.18">
        <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
        <readme>
           
**What it Does**

This tool is part of an update to the CloudMap pipeline (Minevich et al. 2012) to incorporate homozygosity mapping in zebrafish. This tool facilitates the mapping of zebrafish mutants from WGS or RNA-Seq data using bulk segregant homozygosity mapping. As input it takes a VCF list of variants (usually quality filtered for Q200 with WT SNPs/indels removed). This file is produced when running the CloudMap zebrafish pipeline. It plots an adjusted homozygosity ratio such that a high ratio indicates mapping region. It outputs an HTML file with combined and individual chromosome plots as PDFs. The adjusted homozygosity ratio is calculated as described in:

IN SUBMISSION

       </readme>
</tool_dependency>