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==== using a VCF reference panel ====
==== using a VCF reference panel ====
minimac2 --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results
minimac2 --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200
--vcfchr 20 --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
'''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
| <code>--vcfReference </code>
| <code>--vcfReference </code>
| This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.
| This option specifies that the provided --refHaps file is provided in VCF format , no --refSNPs file needed.
|-
| <code>--vcfchr </code>
| Chromosome for which we will carry out imputation.
|-
|-
| <code>--rs </code>
| <code>--rs </code>
