[course homepage]

Problem Set 3 - Complex Traits

[Problem Set 3 PDF]

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/

You should make a directory for problem set 3 in your working directory with subdirectories for code and results:

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

To see how these files were created from the original 1000 Genomes file, see:

• /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