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comparison EMS_VariantDensityMapping.xml @ 9:58a3878549ef draft

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date Mon, 25 Jun 2012 16:09:09 -0400
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1 <tool id="ems_variant_density_mapping" name="CloudMap: EMS Variant Density Mapping">
2 <description>Map a mutation by linkage to regions of high mutation density using WGS data</description>
3 <command interpreter="python">EMS_VariantDensityMapping.py --snp_vcf $snp_vcf --ylim $ylim --hist_color "$hist_color" --standardize $standardize --ems $ems --output $output </command>
4 <inputs>
5 <param name="snp_vcf" type="data" format="vcf" label="VCF of SNPs" help="Takes a VCF file of WGS SNPs present in a C.elegans mutant strain that has been backcrossed to its (pre-mutagenesis) starting strain"/>
6 <param name="ylim" size = "15" type="integer" value="200" label="Y-axis upper limit"/>
7 <param name="hist_color" size = "15" type="text" value="darkgray" label="Color for 1Mb bins" help="See below for list of supported colors"/>
8 <param name="standardize" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Standardize X-axis" help="Frequency plots from separate chromosomes will have uniform X-axis spacing for comparison"/>
9 <param name="ems" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Filter for most common EMS-induced variants (G/C—>A/T)"/>
10 </inputs>
11 <outputs>
12 <data name="output" type="text" format="pdf" />
13 </outputs>
14 <requirements>
15 <requirement type="python-module">sys</requirement>
16 <requirement type="python-module">optparse</requirement>
17 <requirement type="python-module">csv</requirement>
18 <requirement type="python-module">re</requirement>
19 <requirement type="python-module">decimal</requirement>
20 <requirement type="python-module">rpy</requirement>
21 </requirements>
22 <tests>
23 <param name="snp_vcf" value="" />
24 <output name="output" file="" />
25 </tests>
26 <help>
27 **What it does:**
28
29 This tool is part of the CloudMap pipeline for analysis of mutant genome sequences. For further details, please see `Gregory Minevich, Danny Park, Richard J. Poole, Daniel Blankenberg, Anton Nekrutenko, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__
30
31 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
32
33 CloudMap workflows, shared histories and reference datasets are available at the `CloudMap Galaxy page`__
34
35 .. __: https://test.g2.bx.psu.edu/u/gal40/p/cloudmap
36
37 Following the approach detailed in Zuryn et al., Genetics 2010, this tool plots histograms of variant density in a mutant C.elegans strain that has been backcrossed to its (pre-mutagenesis) starting strain. Common (i.e. non-phenotype causing) variants present in multiple WGS strains **with the same background** should first be subtracted using the GATK tool *Select Variants*.
38
39 Sample output where LG III shows linkage to the causal mutation is shown below. In this example, common variants from another strain have been subtracted and remaining variants have been filtered for most common EMS-induced mutations i.e. G/C --> A/T):
40
41 .. image:: http://biochemistry.hs.columbia.edu/labs/hobert/CloudMap/EMS_Variant_Density_750px.png
42
43
44
45
46
47 The experimental approach is detailed in Figure 1a from Zuryn et al., Genetics 2010:
48
49 .. image:: http://biochemistry.hs.columbia.edu/labs/hobert/CloudMap/Zuryn_2010_Genetics_Fig1a.pdf
50
51
52 Subtracting common (non-phenotype causing) variants from more whole genome sequenced strains (using GATK Tools *Select Variants*) will result in less noise and a tighter mapping region. Additional backcrosses will also result in a smaller mapping region.
53
54 ------
55
56 **Settings:**
57
58 .. class:: infomark
59
60 Supported colors for data points and loess regression line:
61
62 http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf
63
64 http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf
65
66
67
68
69 .. class:: warningmark
70
71 This tool requires that the statistical programming environment R has been installed on the system hosting Galaxy (http://www.r-project.org/). If you are accessing this tool on Galaxy via the Cloud, this does not apply to you.
72
73 ------
74
75 **Citation:**
76
77 This tool is part of the CloudMap package from the Hobert Lab. If you use this tool, please cite `Gregory Minevich, Danny Park, Richard J. Poole, Daniel Blankenberg, Anton Nekrutenko, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__
78
79 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
80
81 Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)
82
83 </help>
84 </tool>