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Revision as of 18:47, 27 August 2012
, 18:47, 27 August 2012→Reference Haplotypes
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ MaCH download page]. In our hands, it is ideal to always use the most recent release since generation of additional sequence data, improvements in variant discovery, genotyping and haplotyping strategies typically result in noticeable improvements in data quality. When this page was written, the most recent release of 1000 Genomes project haplotypes was the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G.2012-03-14.html Integrated Phase I release], including 1092 individuals. We recommend to use the reduced GIANT all population panel (no monomorphic and singleton sites)
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ MaCH download page]. In our hands, it is ideal to always use the most recent release since generation of additional sequence data, improvements in variant discovery, genotyping and haplotyping strategies typically result in noticeable improvements in data quality. When this page was written, the most recent release of 1000 Genomes project haplotypes was the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G.2012-03-14.html Integrated Phase I release], including 1092 individuals. We recommend to use the reduced GIANT all population panel (no monomorphic and singleton sites)
[ftp://share.sph.umich.edu/1000genomes/fullProject/2012.03.14/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz]
[ftp://share.sph.umich.edu/1000genomes/fullProject/2012.03.14/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz]
Furthermore, we provide also a [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002793 Metabochip] specific reference panel [ftp://share.sph.umich.edu/1000genomes/fullProject/2012.03.14/GIANT.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz GIANT.metabo.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz]. This panel saves a lot of time, since it focuses on the well-imputable fine-mapping regions.
== Minimac Imputation ==
== Minimac Imputation ==
