VCF by CDS Filter and Annotator

A lightweight Windows x64 GUI app that fliters a vcf file to contain only coding regions and adds coding sequence identifier information

Citations:

When using this software Cite the following:

1. Garrison, E., Kronenberg, Z. N., Dawson, E. T., Pedersen, B. S., & Prins, P. (2022). A spectrum of free software tools for processing the VCF variant call format: Vcflib, bio-vcf, cyvcf2, hts-nim and slivar. PLOS Computational Biology, 18(5), e1009123. doi: 10.1371/journal.pcbi.1009123
2. Li, H., & Rong, J. (2021). Bedtk: Finding interval overlap with implicit interval tree. Bioinformatics, 37(9), 1315–1316. doi: 10.1093/bioinformatics/btaa827
3. Tsiouri, O., (2025). VCF by CDS Filter and Annotator: A lightweight Windows x64 GUI app that fliters a vcf file to contain only coding regions and adds coding sequence identifier information. GitHub https://github.com/olgatsiouri1996/VCF-by-CDS-Filter-and-Annotator

Installation

1. From the Releases tab download gff2bed_features.zip extract it and move it to:

C:\Windows\System32

2. Install bedtk

3. Install Windows Subsystem for Linux

Note: the following installation steps will be performed on Windows Subsystem for Linux

4. Install linuxbrew dependences:

sudo apt install build-essential procps curl file git

5. Install linuxbrew:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

6. Add linuxbrew to PATH:

echo 'eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"' >> ~/.bashrc && source ~/.bashrc

7. Make link of vcfannotate to /usr/local/bin:

sudo ln -s /home/linuxbrew/.linuxbrew/bin/vcfannotate /usr/local/bin/vcfannotate

8. From the Releases tab download the GUI app VCF.by.CDS.Filter.and.Annotator.zip and extract it

Usage

1. Add a gff/gff3 file and a vcf file in a folder with no other files inside:

   • Example vcf file here
   • Example gff file from NCBI Genomes(Genbank) with accession: GCA_000002655

2. In the gff file replace the chromosome names with those of the vcf file:

   NCBI Chr	VCF Chr
   CM00169.1	I
   CM00170.1	II
   CM00171.1	III
   CM00172.1	IV
   CM00173.1	V
   CM00174.1	VI
   CM00175.1	VII
   CM00176.1	VIII

3. Then open VCF by CDS Filter and Annotator.exe and click Browse to navigate to the folder you put the gff/gff3 file the vcf file.

4. Click Filter vcf to run the app.

5. You will be notified when the program is Finished.

6. Example output can be seen here