<tool id="hgv_ldtools" name="LD" version="1.0.0">
  <description>linkage disequilibrium and tag SNPs</description>

  <command interpreter="bash">
    ldtools_wrapper.sh rsquare=$rsquare freq=$freq input=$input output=$output
  </command>

  <inputs>
    <param format="tabular" name="input" type="data" label="Dataset"/>
    <param name="rsquare" label="r&lt;sup&gt;2&lt;/sup&gt; threshold" type="float" value="0.64">
      <validator type="in_range" message="rsquare must be in range [0.00, 1.00]" min="0.00" max="1.00" />
    </param>
    <param name="freq" label="Minimum allele frequency threshold" type="float" value="0.00">
      <validator type="in_range" message="freq must be in range (0.00, 0.50]" min="0.00" max="0.50" />
    </param>
  </inputs>

  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="ldInput1.txt" />
      <param name="rsquare" value="0.64" />
      <param name="freq" value="0.00" />
      <output name="output" file="ldOutput1.txt" />
    </test>
  </tests>

  <help>
**Dataset formats**

The input and output datasets are tabular_.
(`Dataset missing?`_)

.. _tabular: ./static/formatHelp.html#tab
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

This tool can be used to analyze the patterns of linkage disequilibrium
(LD) between polymorphic sites in a locus.  SNPs are grouped based on the
threshold level of LD as measured by r\ :sup:`2` (regardless of genomic
position), and a representative "tag SNP" is reported for each group.
The other SNPs in the group are in LD with the tag SNP, but not necessarily
with each other.

The underlying algorithm is the same as the one used in ldSelect (Carlson
et al. 2004).  However, this tool is implemented to be much faster and more
efficient than ldSelect.

The input is a tabular file with genotype information for each individual
at each SNP site, in exactly four columns: site ID, sample ID, and the
two allele nucleotides.

-----

**Example**

- input file::

    rs2334386  NA20364  G  T
    rs2334386  NA20363  G  G
    rs2334386  NA20360  G  G
    rs2334386  NA20359  G  G
    rs2334386  NA20358  G  G
    rs2334386  NA20356  G  G
    rs2334386  NA20357  G  G
    rs2334386  NA20350  G  G
    rs2334386  NA20349  G  G
    rs2334386  NA20348  G  G
    rs2334386  NA20347  G  G
    rs2334386  NA20346  G  G
    rs2334386  NA20345  G  G
    rs2334386  NA20344  G  G
    rs2334386  NA20342  G  G
    etc.

- output file::

    rs2238748  rs2793064,rs6518516,rs6518517,rs2283641,rs5993533,rs715590,rs2072123,rs2105421,rs2800954,rs1557847,rs807750,rs807753,rs5993488,rs8138035,rs2800980,rs2525079,rs5992353,rs712966,rs2525036,rs807743,rs1034727,rs807744,rs2074003
    rs2871023  rs1210715,rs1210711,rs5748189,rs1210709,rs3788298,rs7284649,rs9306217,rs9604954,rs1210703,rs5748179,rs5746727,rs5748190,rs5993603,rs2238766,rs885981,rs2238763,rs5748165,rs9605996,rs9606001,rs5992398
    rs7292006  rs13447232,rs5993665,rs2073733,rs1057457,rs756658,rs5992395,rs2073760,rs739369,rs9606017,rs739370,rs4493360,rs2073736
    rs2518840  rs1061325,rs2283646,rs362148,rs1340958,rs361956,rs361991,rs2073754,rs2040771,rs2073740,rs2282684
    rs2073775  rs10160,rs2800981,rs807751,rs5993492,rs2189490,rs5747997,rs2238743
    rs5747263  rs12159924,rs2300688,rs4239846,rs3747025,rs3747024,rs3747023,rs2300691
    rs433576   rs9605439,rs1109052,rs400509,rs401099,rs396012,rs410456,rs385105
    rs2106145  rs5748131,rs2013516,rs1210684,rs1210685,rs2238767,rs2277837
    rs2587082  rs2257083,rs2109659,rs2587081,rs5747306,rs2535704,rs2535694
    rs807667   rs2800974,rs756651,rs762523,rs2800973,rs1018764
    rs2518866  rs1206542,rs807467,rs807464,rs807462,rs712950
    rs1110661  rs1110660,rs7286607,rs1110659,rs5992917,rs1110662
    rs759076   rs5748760,rs5748755,rs5748752,rs4819925,rs933461
    rs5746487  rs5992895,rs2034113,rs2075455,rs1867353
    rs5748212  rs5746736,rs4141527,rs5748147,rs5748202
    etc.

-----

**Reference**

Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. (2004)
Selecting a maximally informative set of single-nucleotide polymorphisms for
association analyses using linkage disequilibrium.
Am J Hum Genet. 74(1):106-20. Epub 2003 Dec 15.

  </help>
</tool>