Metadata-Version: 2.1
Name: vbtools
Version: 0.1.0
Summary: A pipeline for analyzing fungal genomic data
Home-page: https://github.com/broadinstitute/vbtools
Author: Xiao Li
Author-email: xiaoli@broadinstitute.org
License: MIT
Project-URL: Bug tracker, https://github.com/broadinstitute/vbtools/issues
Project-URL: Documentation, https://github.com/broadinstitute/vbtools/README.md
Description: # vbtools: a variant benchmark tool to compare VCFs with a consensus set
        ## Install
        Before installation, make sure [conda](https://docs.conda.io/en/latest/miniconda.html) is under your `PATH`. Conda installation [here](https://docs.conda.io/en/latest/miniconda.html).
        
        ```sh
        # 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.
        ```sh
        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](https://samtools.github.io/hts-specs/VCFv4.2.pdf).
        
        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.
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Natural Language :: English
Description-Content-Type: text/markdown
