genimpute

Integrated tool set to perform quality control and imputation of diploid genotypes

Quick start

git clone https://github.com/scimerc/genimpute.git && cd genimpute

Run

genimpute.sh -h

to get usage instructions. genimpute.sh's default settings deploy a minimal configuration.

Run

make run_example

to run imputation on a small test data set.

Configuration

Below is a configuration file example to submit genimpute.sh jobs to a slurm scheduler using a set of reference haplotypes (necessary for imputation). The cluster nodes are expected to have 256GB of memory distributed over 64 computing cores.

# custom configuration file for slurm

execommand='sbatch --account=myaccount'
igroupsize=500
plinkctime=12:00:00
plinkmem=12000
refprefix=hrc.r1-1.ega.grch37
snodecores=64
snodemem=256000

Requirements

• Linux
• Bash

NOTE: Before imputation -- and advisably also before quality control -- reference maps and haplotypes may have to be pre-processed in order to ensure full compatibility with genimpute.sh. The scripts mapproc.sh and refproc.sh perform the necessary pre-processing steps on genetic map and reference haplotypes, respectively.

Authors

Written by Francesco Bettella and Florian Krull based on a deCODE genetics protocol adapted by Sudheer Giddaluru.