Difference between revisions of "ChunkChromosome"
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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 two commands: | ||
− | <source lang=" | + | <source lang="bash"> |
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 | 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 | 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 |
Revision as of 07:23, 5 August 2011
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 1000 Genomes Imputation using MaCH and minimac. Typically, you'd accomplish this by running the two commands:
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