Chrom_Sprim_Visual

This tool aids in S Prime analysis by providing pairwise comparision visual tools. This is helpful in figuring out which populations have more common shared ancestry based on proportion of shared introgressed segments.

Activate virtual environment

python3 -m venv env

source env/bin/activate

Packages that need to be installed

To install packages, you can use pip or pip 3

pip3 install -r requirements.txt 

Make sure the location to which packages are installed are on PATH

export PATH=/path/to/directory:$PATH

If not using own files

• Clone repository
• Locate directory

type

  bokeh serve --show .

if facing issues even after installing the necessary packages, type

  python -m bokeh serve --show .

or

python3 -m bokeh serve --show .

• To view how preprocessing and analysis was done, check the Jupyter_Deliverables folder for the Overall_finale jupyter notebooks

Format of input files

Sprime files

• Sprime files should have population name and chromosome name included in filename

Json file

• Ensure population names are stored in a json file

Populations and codes

CHB Han Chinese Han Chinese in Beijing, China JPT Japanese Japanese in Tokyo, Japan CHS Southern Han Chinese Han Chinese South CDX Dai Chinese Chinese Dai in Xishuangbanna, China KHV Kinh Vietnamese Kinh in Ho Chi Minh City, Vietnam CHD Denver Chinese Chinese in Denver, Colorado (pilot 3 only)

CEU CEPH Utah residents (CEPH) with Northern and Western European ancestry TSI Tuscan Toscani in Italia GBR British British in England and Scotland FIN Finnish Finnish in Finland IBS Spanish Iberian populations in Spain

YRI Yoruba Yoruba in Ibadan, Nigeria LWK Luhya Luhya in Webuye, Kenya GWD Gambian Gambian in Western Division, The Gambia MSL Mende Mende in Sierra Leone ESN Esan Esan in Nigeria

ASW African-American SW African Ancestry in Southwest US
ACB African-Caribbean African Caribbean in Barbados MXL Mexican-American Mexican Ancestry in Los Angeles, California PUR Puerto Rican Puerto Rican in Puerto Rico CLM Colombian Colombian in Medellin, Colombia PEL Peruvian Peruvian in Lima, Peru

GIH Gujarati Gujarati Indian in Houston, TX PJL Punjabi Punjabi in Lahore, Pakistan BEB Bengali Bengali in Bangladesh STU Sri Lankan Sri Lankan Tamil in the UK ITU Indian Indian Telugu in the UK

Once done, deactivate environment

deactivate