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== Usage ==
== Usage ==
Suppose you plan to run [[Minimac: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation]] using [[MaCH]] and [[minimac]]. Typically, you'd accomplish this by running the two commands:
Suppose you plan to run [[Minimac: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation]] using [[MaCH]] and [[minimac]]. Typically, you'd accomplish this by running the following commands:
<source lang="bash">
<source lang="bash">
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr1
awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps
minimac --refHaps 1000genomes.chr1.hap.gz --refSnps 1000genomes.chr1.snps --haps chr1.hap.gz --snps chr1.snps --rounds 5 --states 200 --prefix imputation-results
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr1.haps
minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps --snps chr1.snps --rounds 5 --states 200 --prefix imputation-results
</source>
</source>
These commands would haplotype (with MaCH) and then impute (with Minimac) an entire chromosome. While the process works, it can be rather time consuming for large chromosomes and large numbers of individuals. ChunkChromosome allows the process to be streamlined by running different portions of each chromosome in parallel.
== Download ==
== Download ==
