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Minimac: 1000 Genomes Imputation Cookbook

64 bytes added, 18:13, 6 August 2012
X Chromosome Imputation
Impute females and males separately
minimac --refHaps chrX.no.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps females.hap --snps females.snps minimac --refHaps chrX.no.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps males.hap --snps males.snps
=== 3. Impute pseudo-autosomal part by sex ===
Impute females and males separately
minimac --refHaps chrX.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps females.hap --snps females.snps minimac --refHaps chrX.auto.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --vcfReference --haps males.hap --snps males.snps
== Imputation quality evaluation ==
369
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