Problem Set 3 - Complex Traits
Overview
Data files and code templates for this problem set are available on comet at:
/oasis/projects/nsf/csd524/mgymrek/data/ps3/
/oasis/projects/nsf/csd524/mgymrek/templates/ps3/
mkdir /oasis/projects/nsf/csd524/$USER/ps3
mkdir /oasis/projects/nsf/csd524/$USER/ps3/code
mkdir /oasis/projects/nsf/csd524/$USER/ps3/results
PS3 data
The data directory contains the following files you will use in the problem set:ps3_gwas.bed
ps3_gwas.bim
ps3_gwas.ped
ps3_gwas.map
ps3_gwas.fam
ps3_gwas.phen
eyecolor_snps_irisplex.bed
ps3_pred_eyecolor.vcf.gz
ps3_pred_eyecolor.vcf.gz.tbi
/oasis/projects/nsf/csd524/mgymrek/templates/ps3/preprocess_gwa.sh
/oasis/projects/nsf/csd524/mgymrek/templates/ps3/preprocess_prediction.sh
PS3 templates
The templates directory contains:run_ps3_gwas_plink.sh
ps3_manhattan.py