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Minimac: 1000 Genomes Imputation Cookbook

317 bytes added, 18:11, 6 August 2012
2. Impute non-pseudo-autosomal part by sex
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 ===
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