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Minimac: 1000 Genomes Imputation Cookbook

65 bytes added, 16:04, 3 October 2012
Further Time Savings
== Further Time Savings ==
=== Target based chunking ===
The recipe above imputes whole chromosomes, one a time. A further time savings is possible by imputing chromosomes in chunks, a process that can be facilitated using the [[ChunkChromosome]] tool. This tool automates some of the manual editing steps that would be required to divide each chromosome into more manageable chunks. It also interfaces with minimac to ensure SNPs that overlap between chunks are only imputed once.
Although the loss in accuracy will typically be small, analyses of small chromosome chunks will necessarily result in slightly less accurate results. The differences will be large in populations where haplotype sharing is expected to extend further (for example, in Finland and Sardinia we find that haplotypes can be estimated accurately over several megabases and focusing on small chunks of chromosome will make these matches harder to identify).
=== Reference based chunking ===
== X Chromosome Imputation ==

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