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, 06:24, 28 January 2015
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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 |
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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 | | '''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 |
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| | <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> |