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

Install

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

# clone this repo
git clone git@github.com:broadinstitute/vbtools.git

# 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

Usage

You can use following command to benchmark a VCF against a reference/consensus VCF.

vcfbench.py -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.