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

== Datasets ==
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
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 
The study panel is an artificial genotype dataset. Created by