IMPUTE-PIPELINE-MIGNOT-LAB

A pipeline to impute plink genotypes to 1000 Genomes phase 1 this is only applicable to stanford genomics cluster environment

An example command would be (plinkfile without extension)

./IMPUTE_PIPELINE_V1_AA_FEB2018.sh plinkfile

Name		Name	Last commit message	Last commit date
Latest commit History 22 Commits
CAT_IMPUTE_FILES_STEP4.sh		CAT_IMPUTE_FILES_STEP4.sh
IMPUTE_HEADCOMMAND_STEP3.py		IMPUTE_HEADCOMMAND_STEP3.py
IMPUTE_LOOP_PHASE1_STEP3.sh		IMPUTE_LOOP_PHASE1_STEP3.sh
IMPUTE_PIPELINE_V1_AA_FEB2018.sh		IMPUTE_PIPELINE_V1_AA_FEB2018.sh
LICENSE		LICENSE
PLINK_SPLIT_CHR_STEP1.sh		PLINK_SPLIT_CHR_STEP1.sh
README.md		README.md
SHAPEIT_ARRAY_TASK_STEP2.sh		SHAPEIT_ARRAY_TASK_STEP2.sh
chr_sizes.txt		chr_sizes.txt