---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: VCF Splitting - C.virginica VCF Using BCFtools
date: '2019-01-02 07:39'
tags:
  - bcftools
  - Crassostrea virginica
  - Eastern oyster
  - tabix
categories:
  - 2019
  - Miscellaneous
---
[Steven asked that I split up a _Crassostrea virginica_ VCF file](https://github.com/RobertsLab/resources/issues/528):

- [Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz (31GB)](http://gannet.fish.washington.edu/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz)


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](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190103_swoose_C.virginica_vcf_splitting.ipynb)

---

# RESULTS

Output folder:

- [20190103_Cvirginica_vcf_splitting](http://gannet.fish.washington.edu/Atumefaciens/20190103_Cvirginica_vcf_splitting)

Will let Steven know this is complete and close out [GitHub issue]((https://github.com/RobertsLab/resources/issues/528)).

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