linkage disequilibrium and tag SNPs
ldtools_wrapper.sh rsquare=$rsquare freq=$freq input=$input output=$output
**Dataset formats**
The input and output datasets are tabular_.
(`Dataset missing?`_)
.. _tabular: ./static/formatHelp.html#tab
.. _Dataset missing?: ./static/formatHelp.html
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**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.
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**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.
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**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.