Overview of process:
Sorted and bgzipped file.
Indexed sorted file with
Filled AN/AC values with
bcftoolsAN/AC fill plugin.
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):
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!