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Advanced Customization

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Jie Huang edited this page Nov 17, 2021 · 3 revisions

#1. Download & Run: for advanced users

Prepare:

  • Conda (or Miniconda), Git, for installing python packages.

  • PLINK1.9 and PLINK2.0, named "plink" and "plink2" respectively

    set in "PATH", or in the "plink_dir" of the PAGEANT/bin/config.ini file.

  • For Mac-OS, install Homebrew, and then run "brew install zbar llvm". For Linux, run "sudo apt-get install libzbar0".

Download:

git clone https://github.com/jielab/pageant.git
cd pageant
git pull # for getting an updated version
conda env create -f environment_linux.yml 
# "environment_macos.yml" for Mac-OS, "environment_win.yml" for Windows

  • Download 1000 genomes project (G1K) genotype, to be used as population reference. The basic version of PAGEANT comes with a subset of the G1K data that includes all SNPs used in the genetic report.

Run:

GUI version:

  • For Windows user using Ubuntu Linux, an upgrade to Windows 11 is recommended, which supports WSL GUI. In Windows Powershell, run "wsl --update" to get the latest version.
conda activate pageant
python ./GUI.py

Command line version:

conda activate pageant
python ./pageant.py -n test -i ./personal_genome/HG001.vcf.gz -o output

For 3 APIs:

  • for umap, first download the sample information file if using 1000 genomes as reference.
  • for add_rsid, first download the rsids-v*-hg*.tsv.gz file towards the end of pheweb resource page. Make sure that the chromosome and positions in the input GWAS file is sorted first, by using sort -k 1,1n -k 2,2n.
  • for liftOver, first download the chain files, for hg19 and/or for hg38.
  • for help: python pageant.py [API-NAME] --help
- conda activate pageant
- python pageant.py umap -s HG001.vcf.gz -p g1k.vcf.gz -m g1k_samples.txt
- python pageant.py add_rsid -i test.gwas.gz --chr chr --pos pos -d rsids-v154-hg19.tsv.gz -o new.gwas.gz
- python pageant.py liftOver -i test.gwas.gz --chr chr --pos pos -c hg38ToHg19.over.chain.gz -o new.GWAS.gz
- python pageant.py qr_code -s fingerprint_snps.txt -k key

#2. Customize PAGEANT

The folder structures of PAGEANT is shown below. Advanced users could also follow this structure to customize the genetic report.

For example, under "algorithm database" folder, there are 3 files for each trait folder: TRAIT.desc.txt for description text, TRAIT.jpg for a representative picture, TRAIT.snps.ref for a list of SNPs used and the relevant calculation rules.

For qualitative traits, the TRAIT.snps.ref has four columns: SNP, genotype, matched, unmatched; For quantitative trait, the TRAIT.snps.ref file requires three columns: SNP, EA (effect allele), BETA or OR (effect size).

Folder Structure


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