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