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== using a VCF reference panel ==
== using a VCF reference panel ==
minimac --vcfReference --refHaps ref.vcf.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
minimac --vcfReference --refHaps ref.vcf.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
Note: GWAS SNPs (file --snps target.snps.gz) have to be in the chr:pos format e.g. 1:1000 and on build37/hg19
== using a MaCH reference panel ==
== using a MaCH reference panel ==
minimac --refHaps ref.hap.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
minimac --refHaps ref.hap.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
