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== 2. Prepare VCF file with genotypes / dosages ==
== 2. Prepare VCF file with genotypes / dosages ==
EPACTS requires input genotype / doseage information in VCF format. From minimac or Impute2, you wil start with your imputed dosage file.
EPACTS requires input genotype / dosage information in VCF format. From minimac or Impute2, you wil start with your imputed dosage file.
=== A. Convert dosage file into VCF format ===
=== A. Convert dosage file into VCF format ===
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download the tool from [http://www.sph.umich.edu/csg/cfuchsb/dose2vcf_v0.4.tgz here]. If you used rs numbers during imputation, you can find mapping tables ready for dose2vcf [http://www.sph.umich.edu/csg/cfuchsb/mapping_rs_ALL.GIANT.phase1_release_v3.20101123.tgz here (214 Mb) ]
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download the tool from [http://www.sph.umich.edu/csg/cfuchsb/dose2vcf_v0.4.tgz here]. If you used rs numbers during imputation, you can find mapping tables ready for dose2vcf [http://www.sph.umich.edu/csg/cfuchsb/mapping_rs_ALL.GIANT.phase1_release_v3.20101123.tgz here (214 Mb) ]
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To run the wrapper program, use the following command
To run the wrapper program, use the following command
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Note that for longer chromosomes, the program is quite memory intensive. In this case, please convert dosages in shorter sections of the chromosome. For example, if the imputation was performed by sections, then convert these sections to vcf first, and then merge the vcf files together using vcftools [http://vcftools.sourceforge.net/docs.html#concat vcf-concat]:
Note that for longer chromosomes, the program is quite memory intensive. In this case, please convert dosages in shorter sections of the chromosome. For example, if the imputation was performed by sections, then convert these sections to vcf first, and then merge the vcf files together using vcftools [http://vcftools.sourceforge.net/docs.html#concat vcf-concat]:
=== B. bgzip and tabix VCF files ===
=== B. bgzip and tabix VCF files ===
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
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If the VCF file is separated by chromosome, the VCF file must contain the string "chr1" in the chromosome 1 file, and corresponding chromosome name for other chromosomes.<br>Sample IDs in the VCF file must be consistent to those from PED file
If the VCF file is separated by chromosome, the VCF file must contain the string "chr1" in the chromosome 1 file, and corresponding chromosome name for other chromosomes.<br>Sample IDs in the VCF file must be consistent to those from PED file
== 3. Prepare PED file for phenotypes and covariates ==
== 3. Prepare PED file for phenotypes and covariates ==
