Name		Name	Last commit message	Last commit date
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1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.bed		1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.bed
1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.bim		1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.bim
1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.fam		1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.fam
HM3_thinned_autosomal_overlap.bed		HM3_thinned_autosomal_overlap.bed
HM3_thinned_autosomal_overlap.bim		HM3_thinned_autosomal_overlap.bim
HM3_thinned_autosomal_overlap.fam		HM3_thinned_autosomal_overlap.fam
README.md		README.md
data.RData		data.RData
data.bed		data.bed
data.bim		data.bim
data.fam		data.fam
hapmap3.pdf		hapmap3.pdf
hapmap3_comparison.pdf		hapmap3_comparison.pdf
hapmap3_pairs.pdf		hapmap3_pairs.pdf
plot.R		plot.R
relationships_w_pops_121708.txt		relationships_w_pops_121708.txt
run.sh		run.sh
test_cca.R		test_cca.R
test_pca.R		test_pca.R

README.md

Datasets

Files: HM3_thinned_autosomal_overlap.{bed,bim,fam}

This dataset consists of 957 founders extracted from the HapMap3 phase III data (http://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format), hapmap3_r2_b36_fwd.consensus.qc.poly.{bed,bim,fam}, using PLINK options:

--bfile hapmap3_r2_b36_fwd.consensus.qc.poly
--maf 0.01
--geno 0.01
--mind 0.01
--hwe 5e-6
--filter-founders
--autosome

The data was then LD-thinned with PLINK using

--indep-pairwise 1000 10 0.02

The final dataset has 14,079 autosomal SNPs.

Files: 1kg.ref.phase1_release_v3.20101123_thinned_autosomal_overlap.{bed,bim,fam}

This data contains genotypes for 1,092 individuals from the 1000 Genomes project, for the same 14,079 SNPs from the HapMap3 dataset above.