wiki:Test imputation pipeline


The purpose if this run is to test the efficiency of the existing imputation pipelines in the Grid. To do this we generated artificial data for 5000 samples in the SNP set of the Illumina Hap550 platform. The "Amsterdam" and "Groningen" team should run independently the analysis and locate discrepancies in the analysis and the generated results.



The reference dataset has been created from the raw VCF data of 1000 Genomes data.

Study panel

The study panel is an artificial genotype dataset. It consists of 5000 samples in the SNP 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:
  • Download and install hapgen2:
  • Download the list of SNPs in the Hap550 platform:
  • For the hapgen2 to run we need to specify at least one causal SNP. We selected the first SNP of the dataset (in our case 16539175). In order not to add any genome wide variation in this SNP determine the odds ratio as 1.0:
    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
    • This command requires 80G of memory.
  • Filter the generated gen files with the SNPs from the hap550 file. According to the documentation of hapgen2 you can specify a list of SNPs and limit the generation of the files in these SNPs (the -t option). I didn't use this option and I filtered the generated data afterwards to the positions of hap550 in order to check if the positions indeed matched. Some stats:
    SNPs in 1000Genomes and in Hap550: 546,233
    SNPs in 1000Genomes but not in Hap550: 36,265,509
    SNPs not in 1000Genomes but in Hap550: 935

"Amsterdam" Run

"Groningen" Run

  • The first step is to upload the data in the grid.
  • Use Molgenis - compute to generate the scripts (jdl and sh files)
Last modified 11 years ago Last modified on Feb 17, 2012 2:05:09 PM