annotate SNP_Mapping.xml @ 9:d4aa63bc2ef6

Deleted selected files
author gregory-minevich
date Tue, 27 Mar 2012 11:33:24 -0400
parents d81e15c526ca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
1 <tool id="snp_mapping_using_wgs" name="CloudMap: SNP mapping with WGS data">
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
2 <description>Map a mutation by plotting recombination frequencies resulting from crossing to a highly polymorphic strain</description>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
3 <command interpreter="python">SNP_Mapping.py --sample_pileup $sample_pileup --haw_vcf $haw_vcf --loess_span $loess_span --d_yaxis $d_yaxis --h_yaxis $h_yaxis --points_color $points_color --loess_color $loess_color --output $output --location_plot_output $location_plot_output --standardize $standardize</command>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
4 <inputs>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
5 <param name="sample_pileup" size = "125" type="data" format="pileup" label="WGS Mutant Pileup File" help="WGS pileup file from pooled F2 mutants that have been crossed to a mapping strain. The pileup should contain data from only mapping strain (e.g. Hawaiian) SNP positions" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
6 <param name="haw_vcf" size = "125" type="data" format="vcf" label="VCF of mapping strain (e.g. Hawaiian) SNPs" help="A VCF reference file that contains mapping strain SNP positions and reference base pairs at each position"/>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
7 <param name="loess_span" size = "15" type="float" value=".01" label="Loess span" help="Parameter that controls the degree of data smoothing."/>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
8 <param name="d_yaxis" size = "15" type="float" value=".7" label="Y-axis upper limit for dot plot" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
9 <param name="h_yaxis" size = "15" type="integer" value="500" label="Y-axis upper limit for histogram plot" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
10 <param name="points_color" size = "15" type="text" value="gray27" label="Color for data points" help="See below for list of supported colors"/>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
11 <param name="loess_color" size = "15" type="text" value="red" label="Color for loess regression line" help="See below for list of supported colors"/>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
12 <param name="standardize" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Standardize X-axis" help="Dot plots and histogram plots from separate chromosomes will have uniform X-axis spacing for comparison"/>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
13 </inputs>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
14 <outputs>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
15 <data name="output" type="text" format="tabular" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
16 <data name="location_plot_output" format="pdf" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
17 </outputs>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
18 <requirements>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
19 <requirement type="python-module">sys</requirement>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
20 <requirement type="python-module">optparse</requirement>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
21 <requirement type="python-module">csv</requirement>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
22 <requirement type="python-module">re</requirement>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
23 <requirement type="python-module">decimal</requirement>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
24 <requirement type="python-module">rpy</requirement>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
25 </requirements>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
26 <tests>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
27 <param name="sample_pileup" value="" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
28 <param name="haw_vcf" value="" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
29 <output name="output" file="" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
30 <output name="plot_output" file="" />
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
31 </tests>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
32 <help>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
33 **What it does:**
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
34
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
35 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 and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
36
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
37 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
38
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
39 This tool improves upon the method described in Doitsidou et al., PLoS One 2010 for mapping causal mutations using whole genome sequencing data.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
40
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
41 Sample output for a linked chromosome:
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
42
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
43 .. image:: http://biochemistry.hs.columbia.edu/labs/hobert/CloudMap/Linked_LG_500px.png
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
44
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
45
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
46 The polymorphic Hawaiian strain CB4856 is used as a mapping strain in most cases but in principle any sequenced nematode strain that is significantly different from the mutant strain can be used for mapping. The tool plots the ratio of mapping strain (Hawaiian)/mutant strain (N2) nucleotides at all SNP positions, reflecting the number of recombinants in the sequenced pool of animals. Chromosomes which contain regions of linkage to the causal mutation will have regions where the ratio of mapping strain (Hawaiian)/total reads will be equal to 0. The scatter plots for such linked regions will have a high number of data points lying exactly on the X axis. A loess regression line is plotted through all the points on a given chromosome giving further accuracy to the linked region.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
47
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
48 Each scatter plot has a corresponding frequency plot that displays regions of linked chromosome where 0 ratio SNP positions are concentrated. 1Mb bins for the 0 ratio SNP positions are colored gray by default and .5Mb bins are colored in red.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
49
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
50
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
51 The experimental design required to generate data for the plots is described in Doitsidou et al., PLoS One 2010 Figure 1:
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
52
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
53 .. image:: http://biochemistry.hs.columbia.edu/labs/hobert/CloudMap/Doitsidou_2010_PLoS_Fig.1_500px.png
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
54
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
55
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
56 ------
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
57
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
58 **Input:**
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
59
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
60
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
61 The input pileup files are generated by the SAMTools mpileup tool. Default SAMTools mpileup (and Samtools filter pileup) parameters for mapping quality, base quality and coverage at each SNP position typically yield good results, though users may experiment with filtering SNP data by adjusting these parameters. In our testing, low threshold filtering on base pair quality has been useful in improving accuracy of plots while high threshold filtering on coverage has skewed plot accuracy.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
62
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
63 This tool requires a pileup that has been created at each SNP position using SAMTools mpileup (http://samtools.sourceforge.net/samtools.shtml) and a BED file of all Hawaiian SNP positions. Download Hawaiian SNP positions BED file here:
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
64 http://biochemistry.hs.columbia.edu/labs/hobert/protocols.html
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
65
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
66 The required VCF of mapping strain (e.g. Hawaiian) SNPs is a reference file that contains mapping strain SNP positions and reference base pairs at each position.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
67 (download Hawaiian SNPs VCF from: http://biochemistry.hs.columbia.edu/labs/hobert/protocols.html). You may also make your own VCF of SNP positions following the steps described in the CloudMAP paper.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
68
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
69
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
70 **Output:**
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
71
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
72 The tool also provides a tabular output file that contains a count of the number of reference and alternate SNPs at each mapping strain SNP position as well as the ratio of reference/alternate SNPs. The position of each mapping strain SNP in map units and physical coordinates is also provided in the output file.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
73
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
74
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
75 ------
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
76
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
77 **Settings:**
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
78
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
79 .. class:: infomark
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
80
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
81 Information on loess regression and the loess span parameter:
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
82 http://en.wikipedia.org/wiki/Local_regression
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
83
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
84 .. class:: infomark
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
85
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
86 Based on our testing, we've settled on .01 as a loess span default. Larger values result in smoothing of the line to reflect trends at a more macro level. Smaller values result in loess lines that more closely reflect local data fluctuations. Users looking at chromosome subregions will want to increase the loess span.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
87
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
88 .. class:: infomark
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
89
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
90 Supported colors for data points and loess regression line:
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
91
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
92 http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
93
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
94 http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
95
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
96
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
97
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
98 .. class:: warningmark
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
99
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
100 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.
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
101
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
102
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
103 ------
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
104
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
105 **Citation:**
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
106
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
107 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 and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
108
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
109 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
110
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
111 Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
112
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
113 </help>
d81e15c526ca Uploaded
gregory-minevich
parents:
diff changeset
114 </tool>