Changes

==== using a VCF reference panel  ====

==== using a VCF reference panel  ====

   minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results

   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

'''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

==== using a MaCH reference panel  ====

==== using a MaCH reference panel  ====