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→Imputation into Phased Haplotypes - minimac
minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
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 and include an ''aliases'' file --snpAliase [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz]
