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!!