Dataset formats
The input and output datasets are tabular. (Dataset missing?)
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 r2 (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.