VdCallFormat

A simple plugin to open VCF and BCF files in Visidata using pysam to parse the files.

Installation

1. Install Visidata
2. Install pysam
3. Create the directory:

   mkdir -p ~/.visidata/plugins

5. Download the plugin to the directory creted:

wget -P ~/.visidata/plugins https://raw.githubusercontent.com/rafaeltou/VdCallFormat/refs/heads/main/VdCallFormat.py

7. Add the plugin to ~/.visidatarc:

echo "import plugins.VdCallFormat" >> ~/.visidatarc

Usage

The usage is very simple. Once installed, you just point the Visidata to the vcf(.gz)/bcf file, eg:

vd file.vcf

Options:

--threads=number:

for the number of threads used in the file parsing in cyvcf2. In my tests it doesn't make much difference. the standard value is 4.

--region=chr:posBegin-posEnd:

for specifying the region you want to see. You can use --region=chr:posBegin to see a single position and --region=chr to see an entire chromossome. This option requires your variant file to be indexed, otherwise it will fail. I recommend always using this option if your file is too big, since the visidata will load all of it to the computer's RAM.

Example:

Developed by Rafael Tou (@rafaeltou)