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comparison tools/human_genome_variation/ldtools.xml @ 0:9071e359b9a3

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date Fri, 09 Mar 2012 19:37:19 -0500
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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 <output name="output" file="ldOutput1.txt" />
28 </test>
29 </tests>
30
31 <help>
32 **Dataset formats**
33
34 The 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
44 This 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
46 threshold level of LD as measured by r\ :sup:`2` (regardless of genomic
47 position), and a representative "tag SNP" is reported for each group.
48 The other SNPs in the group are in LD with the tag SNP, but not necessarily
49 with each other.
50
51 The underlying algorithm is the same as the one used in ldSelect (Carlson
52 et al. 2004). However, this tool is implemented to be much faster and more
53 efficient than ldSelect.
54
55 The input is a tabular file with genotype information for each individual
56 at each SNP site, in exactly four columns: site ID, sample ID, and the
57 two 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
105 Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. (2004)
106 Selecting a maximally informative set of single-nucleotide polymorphisms for
107 association analyses using linkage disequilibrium.
108 Am J Hum Genet. 74(1):106-20. Epub 2003 Dec 15.
109
110 </help>
111 </tool>