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):


Output folder:

Will let Steven know this is complete and close out GitHub issue.

Wow! This took a very long time to run; slightly more than four days for the entire process!