Tagger

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description of this run

I want to specify chromosomal landmarks and use a local copy of the HapMap
I want to upload a HapMap genotype file
I want to upload my own genotype data as a PED file
I want to upload my own genotype data which is phased and in Nick Patterson format

chromosomal landmarks
Enter the genomic regions that you want to tag
using NCBI Build 35/UCSC hg17/May 2004 coordinates
Example: chr10:114,700,200..114,916,057
HapMap analysis panel:

This uses the phased HapMap Release 21 (incl. chrX)

YRI: 2,937,220 polymorphic SNPs
CEU: 2,623,164 polymorphic SNPs
CHB+JPT: 2,480,469 polymorphic SNPs
SNP design scores (for preferential SNP picking)
default design scores for all SNPs:
include tag SNPs exclude tag SNPs
 only evaluate these SNPs (do not pick extra tags) exclude all SNPs with design scores <
which alleles do you want to capture? minimum allele frequency
 all SNPs (above frequency threshold)
 only these specified alleles:
for SNPs:
for haplotypes (if you specified any):
Tagger mode r2 threshold
 pairwise
 aggressive (specified multimarker tests)
for SNPs:
for haplotypes (if you specified any):
advanced settings
maximum number of markers in haplotype tests:
LOD score threshold:
maximum number of tries:
maximum tagging distance:
 pick only the N best tags 
minimum distance between tags:  base pairs

Reference

P.I.W. de Bakker, R. Yelensky, I. Pe'er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005) Efficiency and power in genetic association studies. Nature Genetics. 37: 1217-1223

Any questions?

You can contact us at tagger@broad.mit.edu.