Sam’s Notebook: VCF Splitting – C.virginica VCF Using BCFtools

Steven asked that I split up a Crassostrea virginica VCF file:

Overview of process:

  1. Downloaded file.
  2. Gunzipped file.
  3. Sorted and bgzipped file.
  4. Indexed sorted file with tabix.
  5. Filled AN/AC values with bcftools AN/AC fill plugin.
  6. BCFtools to split sorted/filled VCF in to individual VCF files.

The entire process is documented in the Jupyter Notebook linked below.

Jupyter Notebook (GitHub):