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Revision as of 10:12, 5 August 2011
, 10:12, 5 August 2011→Further Time Savings
== Further Time Savings ==
== Further Time Savings ==
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.
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.
Recall that the original analysis script might have looked like this:
Recall that the original analysis script might have looked like this:
wait
wait
</source>
</source>
A modified script, using [[ChunkChromosome]] would look like this:
<source lang="bash">
<source lang="bash">
</source>
</source>
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).
== X Chromosome Imputation ==
== X Chromosome Imputation ==
