Skip to main content

A pipeline for analyzing fungal genomic data

Project description

vbtools: a variant benchmark tool to compare VCFs with a consensus set


Before installation, make sure conda is under your PATH. Conda installation here.

# clone this repo
git clone

# setup conda environment
cd vbtools

conda env create -f env.yml # this will take a few minutes
conda list  # verify new environment was installed correctly

# activate environment
conda activate vbtools

# deactivate the environment when done
conda deactivate

# completely remove the virtual environment
conda remove -name vbtools --all


You can use following command to benchmark a VCF against a reference/consensus VCF. -v <input.vcf> -b <reference.vcf>

--prefix is an option to define prefix to the output files.

Currently, only haploid VCF is supported in the analysis. Diploid VCF will be standardized into haploid before comparison. Input VCF should follow VCF spec v4.2.

Following pre-processing steps are performed on the input VCF before the analysis:

  1. remove unused alleles
  2. remove monomorphic sites
  3. remove sites with heterozygous genotypes
  4. remove non-SNP sites
  5. remove sites with asterisk marks
  6. change diploid to haploid VCF

The script will output:

  1. Site level comparison:
    • a tsv file including number of unique and shared sites.
  2. Sample level comparision:
    • The sample level comparison functionality will be added to the script soon.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

vbtools-0.1.0.tar.gz (5.1 kB view hashes)

Uploaded source

Built Distribution

vbtools-0.1.0-py3-none-any.whl (7.8 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page