From Genome Analysis Wiki
Jump to navigationJump to search
504 bytes added
, 11:15, 5 August 2011
Line 120: |
Line 120: |
| | Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms. | | | Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms. |
| |} | | |} |
− |
| |
− |
| |
− |
| |
− |
| |
| | | |
| == Imputation into Phased Haplotypes == | | == Imputation into Phased Haplotypes == |
Line 172: |
Line 168: |
| === Reference Haplotypes === | | === 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/1000G-2010-08.html MaCH download page]. The most recent set of haplotypes are based on genotype calls from the August 2010 data freeze. | + | 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]. As of this writing, the most recent set of haplotypes are based on genotype calls were generated in May 2011 and are an interim analysis of Project's Phase I data. |
| | | |
| === Imputation quality evaluation === | | === Imputation quality evaluation === |
Line 181: |
Line 177: |
| | | |
| These statistics can be found in the .info file | | These statistics can be found in the .info file |
| + | |
| + | === Additional Sources of Information === |
| + | |
| + | If the combination of MaCH and Minimac still runs too slowly for you, and you have access to a multi-processor compute cluster, you can look at [[ChunkHaplotypes]] page to learn how to conveniently split each chromosome into multiple segments that can be analyzed in parallel. |
| + | |
| + | If you are especially interested in 1000 Genomes Imputation, then you should look at the [[Minimac: 1000 Genomes Imputation Cookbook]]. |
| | | |
| == X Chromosome Imputation == | | == X Chromosome Imputation == |