VCF Splitting - C.virginica VCF Using BCFtools

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

• Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz (31GB)

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):

• 20190103_swoose_C.virginica_vcf_splitting.ipynb

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RESULTS

Output folder:

• 20190103_Cvirginica_vcf_splitting

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!