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 ​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:

The study panel is an artificial genotype dataset. Created by