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Revision as of 03:49, 11 September 2014

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'''Note''': GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19; otherwise, please set the --rs flag
 
'''Note''': GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19; otherwise, please set the --rs flag
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==== using a MaCH reference panel  ====
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  minimac --refHaps ref.hap.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
      
A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:
 
A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:
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=== Additional Sources of Information ===
 
=== Additional Sources of Information ===
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If the combination of MaCH and Minimac still runs too slowly for you, and you have access to a multi-processor compute cluster, you can look at [[ChunkChromosome]] page to learn how to conveniently split each chromosome into multiple segments that can be analyzed in parallel. For information on how to put the resulting chunks back together, see [[Ligate Minimac|this page]].
      
If you are especially interested in 1000 Genomes Imputation, then you should look at the [[Minimac: 1000 Genomes Imputation Cookbook]].
 
If you are especially interested in 1000 Genomes Imputation, then you should look at the [[Minimac: 1000 Genomes Imputation Cookbook]].
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