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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

  1. Install bedtk

  2. Install Windows Subsystem for Linux

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

  1. Install linuxbrew dependences:
sudo apt install build-essential procps curl file git
  1. Install linuxbrew:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  1. Add linuxbrew to PATH:
echo 'eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"' >> ~/.bashrc && source ~/.bashrc
  1. Make link of vcfannotate to /usr/local/bin:
sudo ln -s /home/linuxbrew/.linuxbrew/bin/vcfannotate /usr/local/bin/vcfannotate
  1. 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