Normal PCA (without a reference)

GWASpy allows you to run normal PCA without any reference panel

Below is a code on how you can run normal PCA without a reference via the command-line or inside a Python script Use

1. Command line

   pca --data-dirname data/ --data-basename 1kg_annotated --out-dir data/ --input-type hail --reference grch37 --pca-type normal
   

2. Python (inside a Python script)

   import gwaspy.pca as pca
   pca.pca.pca(data_dirname="data/", data_basename="1kg_annotated",  out_dir="data/",
               input_type="hail", reference="GRCh37", pca_type="normal")