Imputation pipeline used in the mignot lab

This is slurm job dependent pipeline that takes in base plink format bed files, splits them into chromosomes ( 1 to 22) and then phases them using shapeit, after phasing each chromosome is imputed to 1000 genomes phase 3 in 1mb chunks

Dependancies

plink/1.90 shapeit impute2

example command

python imputePipe.py -F plink_binary