Changes

For external users, follow the instruction at [[EPACTS]] page, summarized below.  

For external users, follow the instruction at [[EPACTS]] page, summarized below.  

*Please download the latest version of EPACTS here:  http://www.sph.umich.edu/csg/kang/epacts/download/

*Please download the latest version of EPACTS here:  http://csg.sph.umich.edu//kang/epacts/download/

*Uncompress EPACTS package to the directory you would like to install and then type the following commands

*Uncompress EPACTS package to the directory you would like to install and then type the following commands

=== 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 pseudo VCF format.  Download the tool from [http://www.sph.umich.edu/csg/cfuchsb/dose2vcf_v0.5.gz 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 pseudo VCF format.  Download the tool from [http://csg.sph.umich.edu//cfuchsb/dose2vcf_v0.5.gz here]. If you used rs numbers during imputation, you can find mapping tables ready for dose2vcf [http://csg.sph.umich.edu//cfuchsb/mapping_rs_ALL.GIANT.phase1_release_v3.20101123.tgz here (214 Mb) ]  

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Note that for longer chromosomes, the program is quite memory intensive. &nbsp;In this case, please convert dosages in shorter sections of the chromosome. &nbsp;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. &nbsp;In this case, please convert dosages in shorter sections of the chromosome. &nbsp;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. &nbsp;bgzip and tabix VCF files  ===

=== B. &nbsp;bgzip and tabix VCF files  ===

== 5. &nbsp;Report results<br>  ==

== 5. &nbsp;Report results<br>  ==

For '''analysis 1''', please follow the following results file guidelines: &nbsp; [[Image:1000Genomes march2012 imputation analysis plan 08312012.pdf]]  

For '''analysis 1''', please follow the following results file guidelines: &nbsp; [[Image:1000Genomes_march2012_imputation_analysis_plan_08312012_v2.pdf]] (Updated Dec 14, 2012)

 

 

For '''analyses 2 and 3''', please upload the two epacts.gz files to the FTP server:  

For '''analyses 2 and 3''', please upload the two epacts.gz files to the FTP server: