AncientProxy

This repository features a tool, AncientProxy, that identifies ancient genotyped variants (AGVs) from the Allen Ancient DNA Resource or AADR that occur in linkage disequilibrium (LD) with a variant of interest using data from TopLD. AGVs in LD with a variant of interest are displayed and the results can be downloaded. If a queried variant is an AGV itself, summary data are provided and users can also download the individual genotypes. Bulk data on variants in LD with AGVs can be downloaded here and bulk data on ancient genotypes can be downloaded here. Users can search for variants using genomic position per the GRCh38/hg38 reference assembly or rsID. Please note that each query may take one to two minutes. Questions or comments about this tool? Please email colin.brand@ucsf.edu or tony@capralab.org.

Notes:

• Two measures of LD are available per variant pair: r-squared and D'.
• Variant pairs with r-squared < 0.5 are not displayed in the app; however, all variant pairs where r-squared is $\geq$ 0.2 are available in the downloadable bulk data.
• LD metrics are available for up to four ancestry groups per variant pair: African, East Asian, European, and South Asian.
• Genomic position for AGV-LD variant pairs use the GRCh38/hg38 reference assembly, whereas ancient genotypes downloaded from the app or retrieved from the VCFs use the GRCh37/hg19 reference assembly.
  
  

Quick Start

You can run AncientProxy in three ways:

1. Docker
2. Python virtual environment (pip)
3. Conda environment
   
   

Docker

Build the image

git clone https://github.com/brandcm/AncientProxy.git
cd AncientProxy
open -a "Docker" # start Docker
docker build -t ancientproxy . # build image

Run the container

docker run -p 8050:80 ancientproxy

Then open your browser at http://127.0.0.1:8050.

Python Virtual Environment (pip)

Create the environment

python -m venv {virtual_environment_name}
source {virtual_environment_name}/bin/activate	# On Windows: {virtual_environment_name}\Scripts\activate
pip install -r requirements.txt

Run the app

gunicorn app:server --bind 0.0.0.0:8050 --timeout 120

Then open your browser at http://127.0.0.1:8050.

Conda Environment

Create the environment

git clone https://github.com/brandcm/AncientProxy.git
cd AncientProxy
conda env create -f environment.yml
conda activate ancientproxy

Run the app

gunicorn app:server --bind 0.0.0.0:8050 --timeout 120

Then open your browser at http://127.0.0.1:8050.