Phased Genotypes for Genome-wide Genetic studies
Miaoxin Li
 
 
 

Links of MX Li's tools:

 
Usage: tar −xvf XXX.tar; you are see a number of *.gz files.
Note: all of my tools support the compressed format, *.gz; it is NOT necessary to un-compress a *.gz file before loading it into my tools.
1000G PhaseI v3 Shapeit2 Reference (2010-11 data freeze, 2013-09 haplotypes)
AFR (246 subjects) 1kg.phase1.v3.shapeit2.afr.tar
AMR (181 subjects) 1kg.phase1.v3.shapeit2.amr.tar
ASN (286 subjects) 1kg.phase1.v3.shapeit2.asn.tar
EUR (379 subjects) 1kg.phase1.v3.shapeit2.eur.tar
Note the phased genotypes are compiled from Li Yun's MACH website!
 
1000G Phase3 v5 Shapeit2 Reference The release contains haplotypes on 2,504 samples (#haplotypes = 5,008) for total ~81.2M polymorphic markers released in 2014-09.
Unfortunately, there are less common variants than the above Phase1 V3.
AFR (645 subjects) 1kg.phase3.v5.shapeit2.afr.hg19.tar.gz
AMR (346 subjects) 1kg.phase3.v5.shapeit2.amr.hg19.tar.gz
EAS (497 subjects) 1kg.phase3.v5.shapeit2.eas.hg19.tar.gz
SAS (486 subjects) 1kg.phase3.v5.shapeit2.sas.hg19.tar.gz
EUR (495 subjects) 1kg.phase3.v5.shapeit2.eur.hg19.tar.gz
Note the phased genotypes are compiled from 1000 Genomes Project website!
Comments and suggestions are welcome, please e-mail limx54@gmail.com
 
Miao-xin Li, Department of Psychiatry, Centre for Genomic Sciences, Development and Growth, Centre for Reproduction, Development and Growth, The University of Hong Kong, All rights reserved.