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Table 1 Tools and data installed during MOLGENIS-impute set up

From: Molgenis-impute: imputation pipeline in a box

Step Tool Version Usage
Set up Molgenis-compute 0.0.1 Manage scripts, handle parameters, submit to HPC
Molgenis-pipelines 0.1.0 Imputation BASH scripts and
Pipeline in CSV format
Step 1 Liftover 20120905 Change genomic reference of study panel to the one used by the reference panel (by default from hg18 to hg19)
PLINK 1.07 Update marker position of input files during liftover step
Step 2 SHAPEIT v2.r644 Phasing of study panel
Step 3 Genotype Harmonizer 1.3.1 Perform quality control
Step 4 Bash script   Split data in sample chunks
Step 5 Impute2 v2.3.0 Main imputation tool
Prepare reference panel vcftools 0.1.11 Convert reference panel from VCF format to IMPUTE2
tabix 0.2.6 Compress reference panel VCF files and build index
Step Data Version Usage
Step 1 Hg18 to hg19 chain file   Map positions between hg18 and hg19 genomic reference
Step 2, 3 Subset (chromosome 1, first 10 Mbp) of HapMap data v.3 release 2 Example study panel for imputation
Step 3 Subset (chromosome 1, first 10 Mbp) of 1,000 Genomes project GIANT release Example reference panel for imputation
Step 3 Recombination map for hg19   Calibration of hidden Markov model [13]