convert.vcf

Conversion of VCF to FinalistDX Excel format. This package depends on a custom version of vcf.R package that can parse annotated VCFs produced by VEP and snpEff tools.

Installation

If not yet, first create a new GitHub PAT with permissions for private repository access and save the token

Package

install.packages("remotes")
# Replace "<PAT>" with your GitHub PAT
Sys.setenv(GITHUB_PAT = "<PAT>")
remotes::install_github("DNA-Lab-FNO/convert.vcf")

Command line interface (CLI)

This packages provides a simple CLI script that calls convert_vcf_files_to_finalist() followed by write_output_file(). To install the script on your system, use

convert.vcf::install_cli("/path/to/directory")

For example, you can use:

• /usr/local/bin for system-wide installation
• ~/.local/bin for user-specific installation
  • Note that this directory must be present in your PATH environment variable. If not, run export PATH=${PATH}:~/.local/bin, or put this line in your ~/.bashrc to make it permanent.
• /opt/miniconda3/envs/<env>/bin for installation into a specific conda environment

Usage

In R

After installation see help pages of the functions below (e.g. call ?read_vcf in R)

• read_vcf()
• convert_vcf_files_to_finalist()

From CLI

For available arguments, run convert_vcf.R -h

Example of batch conversion of VCF files into FinalistDX Excel format (note that haplotypecaller and vep are default expected variant calling and variant annotation tools, respectively):

convert_vcf.R \
  --output_file 2024_07_03_Panel_run_4_BRCA202.haplotypecaller.filtered_VEP.xlsx \
  /data/scratch/run_sarek/2024_12_04/2024_07_03_Panel_run_4/BRCA202/results/variant_calling/results/annotation/haplotypecaller/*/*.haplotypecaller.filtered_VEP.ann.vcf.gz