Compare Dante WGS and 23andme genotyping data

Two major goals for this project:

Perform some QC analysis on WGS data from Dante labs.
Optional - Compare 23andme genotyping data to WGS vcf to ensure they actually match.

What does it do?

Perform QC analyses on WGS data
- fastqc
- qualimap
Following are performed when 23andme_file is specified by user in configs/configs.yaml.
- Convert 23andme genotype raw data to vcf format
- Compare calls in Dante WGS vcf to 23andme vcf using rtg vcfeval

Requirements

OS
- macOS (Developed and tested)
- Linux (Not tested but should work)
- Windows (Not tested; coin toss)
Tools
- Anaconda (Miniconda might work as well)
- Snakemake
  - conda install -c bioconda -c conda-forge snakemake

How to run?

Clone or download this repository
- Clone: git clone https://github.com/ManavalanG/personal_genome_analysis
- Download: See here for how to.
cd into repo directory.
- cd /path/to/personal_genome_analysis
Set up config file configs/configs.yaml.
- Rename file configs/example_configs.yaml to configs/configs.yaml
- Edit this file to specify file paths and sample names
Run the snakemake pipeline
- snakemake -k -p --use-conda

Note: Feedbacks are welcome!!