Mignot-Lab/imputePipeline

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

New added support for custom chr range

All chromsomes -CHR 1-22, single chromosome -CHR 1 or a custom range -CHR 2,3,21

Dependancies

plink/1.90 shapeit impute2

example command to impute phase3

python scripts/imputePipe.py -F plink_binary -Ref 3 -CHR 1-22