== Introduction ==
The purpose if this run is to test the efficiency of the existing imputation pipelines in the Grid. 

== Datasets ==
=== Reference ===
The reference dataset has been created from the raw VCF data of 1000 Genomes data.
 * Download VCF files from : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521
 * Export only the SNPs (filter out the indels and SVs) from VCF data by using [http://vcftools.sourceforge.net/ vcftools] and convert to impute2 format (hap and legend format).
{{{
vcftools \
--gzvcf ALL.chr1.phase1_release_v2.20101123.snps_indels_svs.vcf.gz \
--keep-INFO LCSNP --keep-INFO EXSNP --keep-INFO SNP \
--IMPUTE \
--out ALL.chr1.phase1_release_v2.20101123.snps_indels_svs.
}}}
    * Alternatively we coud have used the 1000 Genomes reference panel in impute2 format (legend and hap files) from the impute2 website: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download_reference_data

=== Study panel ===
The study panel is an artificial genotype dataset. The dataset contains the SNPs set of the Illumina Hap550 platform. To generate it we followed the following steps:
 * Download the genetic map of b37 release of human genome from impute2: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download_reference_data
 * Download and install hapgen2: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
 * Download the list of SNPs in the Hap550 platform:
   * Go to : http://genome.ucsc.edu/cgi-bin/hgTables?command=start
   * From the Table combo box select: snpArrayIllumina550
   * Click the "get output" button
 * For the hapgen2 to run we need to specify at least one causal SNP. We selected the first SNP of the dataset : 
{{{
hapgen2 \
-h ALL.chr6.merged_beagle_mach.20101123.snps_indels_svs.genotypes.exported.impute.hap \
-l ALL.chr6.merged_beagle_mach.20101123.snps_indels_svs.genotypes.exported.impute.legend \ 
-m genetic_map_chr6_combined_b37.txt \
-o chr6 \
-dl 16539175 1 1.0 1.0 \
-n 5000 0
}}}
The study panel is an artificial genotype dataset. Created by 
The study panel is an artificial genotype dataset. Created by 
The study panel is an artificial genotype dataset. Created by