root/galaxy-central/tools/human_genome_variation/ldtools.xml

リビジョン 2, 4.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="hgv_ldtools" name="LD" version="1.0.0">
2  <description>linkage disequilibrium and tag SNPs</description>
3
4  <command interpreter="bash">
5    ldtools_wrapper.sh rsquare=$rsquare freq=$freq input=$input output=$output
6  </command>
7
8  <inputs>
9    <param format="tabular" name="input" type="data" label="Dataset"/>
10    <param name="rsquare" label="r&lt;sup&gt;2&lt;/sup&gt; threshold" type="float" value="0.64">
11      <validator type="in_range" message="rsquare must be in range [0.00, 1.00]" min="0.00" max="1.00" />
12    </param>
13    <param name="freq" label="Minimum allele frequency threshold" type="float" value="0.00">
14      <validator type="in_range" message="freq must be in range (0.00, 0.50]" min="0.00" max="0.50" />
15    </param>
16  </inputs>
17
18  <outputs>
19    <data format="tabular" name="output" />
20  </outputs>
21
22  <tests>
23    <test>
24      <param name="input" value="ldInput1.txt" />
25      <param name="rsquare" value="0.64" />
26      <param name="freq" value="0.00" />
27      <param name="output" file="ldOutput1.txt" />
28    </test>
29  </tests>
30
31  <help>
32**Dataset formats**
33
34The input and output datasets are tabular_.
35(`Dataset missing?`_)
36
37.. _tabular: ./static/formatHelp.html#tab
38.. _Dataset missing?: ./static/formatHelp.html
39
40-----
41
42**What it does**
43
44This tool can be used to analyze the patterns of linkage disequilibrium
45(LD) between polymorphic sites in a locus.  SNPs are grouped based on the
46threshold level of LD as measured by r\ :sup:`2` (regardless of genomic
47position), and a representative "tag SNP" is reported for each group.
48The other SNPs in the group are in LD with the tag SNP, but not necessarily
49with each other.
50
51The underlying algorithm is the same as the one used in ldSelect (Carlson
52et al. 2004).  However, this tool is implemented to be much faster and more
53efficient than ldSelect.
54
55The input is a tabular file with genotype information for each individual
56at each SNP site, in exactly four columns: site ID, sample ID, and the
57two allele nucleotides.
58
59-----
60
61**Example**
62
63- input file::
64
65    rs2334386  NA20364  G  T
66    rs2334386  NA20363  G  G
67    rs2334386  NA20360  G  G
68    rs2334386  NA20359  G  G
69    rs2334386  NA20358  G  G
70    rs2334386  NA20356  G  G
71    rs2334386  NA20357  G  G
72    rs2334386  NA20350  G  G
73    rs2334386  NA20349  G  G
74    rs2334386  NA20348  G  G
75    rs2334386  NA20347  G  G
76    rs2334386  NA20346  G  G
77    rs2334386  NA20345  G  G
78    rs2334386  NA20344  G  G
79    rs2334386  NA20342  G  G
80    etc.
81
82- output file::
83
84    rs2238748  rs2793064,rs6518516,rs6518517,rs2283641,rs5993533,rs715590,rs2072123,rs2105421,rs2800954,rs1557847,rs807750,rs807753,rs5993488,rs8138035,rs2800980,rs2525079,rs5992353,rs712966,rs2525036,rs807743,rs1034727,rs807744,rs2074003
85    rs2871023  rs1210715,rs1210711,rs5748189,rs1210709,rs3788298,rs7284649,rs9306217,rs9604954,rs1210703,rs5748179,rs5746727,rs5748190,rs5993603,rs2238766,rs885981,rs2238763,rs5748165,rs9605996,rs9606001,rs5992398
86    rs7292006  rs13447232,rs5993665,rs2073733,rs1057457,rs756658,rs5992395,rs2073760,rs739369,rs9606017,rs739370,rs4493360,rs2073736
87    rs2518840  rs1061325,rs2283646,rs362148,rs1340958,rs361956,rs361991,rs2073754,rs2040771,rs2073740,rs2282684
88    rs2073775  rs10160,rs2800981,rs807751,rs5993492,rs2189490,rs5747997,rs2238743
89    rs5747263  rs12159924,rs2300688,rs4239846,rs3747025,rs3747024,rs3747023,rs2300691
90    rs433576   rs9605439,rs1109052,rs400509,rs401099,rs396012,rs410456,rs385105
91    rs2106145  rs5748131,rs2013516,rs1210684,rs1210685,rs2238767,rs2277837
92    rs2587082  rs2257083,rs2109659,rs2587081,rs5747306,rs2535704,rs2535694
93    rs807667   rs2800974,rs756651,rs762523,rs2800973,rs1018764
94    rs2518866  rs1206542,rs807467,rs807464,rs807462,rs712950
95    rs1110661  rs1110660,rs7286607,rs1110659,rs5992917,rs1110662
96    rs759076   rs5748760,rs5748755,rs5748752,rs4819925,rs933461
97    rs5746487  rs5992895,rs2034113,rs2075455,rs1867353
98    rs5748212  rs5746736,rs4141527,rs5748147,rs5748202
99    etc.
100
101-----
102
103**Reference**
104
105Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. (2004)
106Selecting a maximally informative set of single-nucleotide polymorphisms for
107association analyses using linkage disequilibrium.
108Am J Hum Genet. 74(1):106-20. Epub 2003 Dec 15.
109
110  </help>
111</tool>
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