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