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Jump to navigationJump to searchCreated page with '''ChunkChromosome'' is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices. == Parameters == ''Chu…'
''ChunkChromosome'' is a helper utility for [[minimac]] and [[MaCH]]. It can be used to facilitate analyses of very large datasets in overlapping slices.
== Parameters ==
''ChunkChromosome'' expects three parameters:
* A data file (specified with the '''-d''' command line option), listing all the markers along one chromosome. The data file can optionally include phenotype and other information, which is safely ignored.
* A desired core chunk size, in markers (specified with the '''-n''' command line option and defaulting to 5000 markers).
* A desired overlap between chunks, also in markers (specified with the '''-o''' command line option and defaulting to 500 markers).
== 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:
<source lang="tcsh">
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --rounds 5 --states 200 --prefix results
</source>
== Download ==
== Parameters ==
''ChunkChromosome'' expects three parameters:
* A data file (specified with the '''-d''' command line option), listing all the markers along one chromosome. The data file can optionally include phenotype and other information, which is safely ignored.
* A desired core chunk size, in markers (specified with the '''-n''' command line option and defaulting to 5000 markers).
* A desired overlap between chunks, also in markers (specified with the '''-o''' command line option and defaulting to 500 markers).
== 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:
<source lang="tcsh">
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --rounds 5 --states 200 --prefix results
</source>
== Download ==
