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

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 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]