/precision-medicine

Primary LanguagePython

Test on example data

Download the latest release and update submodules.

download latest release

cd precision-medicine
git submodule init
git submodule update

Create and activate the mamba environment.

mamba env create -f environment.yml
mamba activate pmed

Run the provided example script with toy data.

I have added a very small set of example data in the directory data/example_data/.
This should be an easy way to test that software is working before running on your own dataset.
Make changs to conda directory (and any other necessary paths) in the config file.
Mostly, the snakemake file should already be fit to use example data.

snakemake -c1

Run on real data

Prepare input data.

Create a working directory my_dir with the following structure:

my_dir/
	↳log/
	↳segments/
	↳my_vcf.vcf.gz
	↳my_vcf.vcf.gz.tbi
	↳my_map.txt
	↳config_snakemake.yaml

Prepare input VCF file. ./my_dir/my_vcf.vcf.gz:

  • A single VCF file for all samples and chromosomes. VCF file should be bgzipped and tabixed. Can be less than full genome (e.g. 1 chromosome), if smaller regions are being searched. See example/example_merge.vcf.gz for an example VCF.

Prepare input MAP file. ./my_dir/my_map.map:

  • map file format (column ordering): chromosome variant identifier position in centimorgans base-pair coordinate.
  • This file will serve as reference to the interpolate map script; which will create a new map (interpolated.map) that is used for down stream work.
  • see helper_scripts/reorder_map.sh to fix formatting errors with your map file.
  • see example/example_merge.map, or visit this resource for ready-to-download map files for GRCh36, 37, and 38.

Edit yaml file to include correct file and directory paths.

  • see config_snakemake.yaml for example.
  • We suggest you only modify the following options to reflect appropriate file paths (all other options should be okay to keep as they are, but double checking never hurts 🧐).
conda_dir:
 /home/sdp/miniconda3/envs/pmed/

data_dir:
 example/
vcf_file:
 example/vcfs/example.8-10.vcf.gz
ref_map:
 example/maps/example.8-10.map
out_dir:
 example/segments/

k:
 20
delim:
 space

Edit snakemake file to point to new configs.

configfile: "./my_dir/config_snakemake.yaml"

Running with snakemake

snakemake -c1


TODO: ADD BEFORE PUBLICATION

  • About section. Name of tool. Describtion of tool is a tool to query over biobank-scale genotype data and report KNN for a query individual (or set of query individuals).
  • Installation section.
  • Helper Scripts. ... helper scripts which were part of our research process and could be useful to you while using this tool.
  • Indexing step. Query step
  • Images and figures.
  • Footnotes/acknowledgments.
  • link to publication.
  • citation for publication.