DanielAndreasen / varcomb

Genomic variant combiner

varcomb

This is a tool to work with VCF files, and to combine VCF files from different callers.

Installation

The current recommend way of installing varcomb is using pip:

pip install git+https://github.com/DanielAndreasen/varcomb

Test

Read the tests to understand what this tool does. You can run the tests by cloning this repository:

git clone https://github.com/DanielAndreasen/varcomb
cd varcomb
python setup.py test

Usage

After installation, varcomb is available from the command line:

$ varcomb merge-vcfs \
    --vcf_file1 vcf1.vcf.gz \
    --vcf_file2 vcf2.vcf.gz \
    --vcf_out combined.vcf \
    --ann_vcf1 FIRST \ # Optional
    --ann_vcf2 SECOND  # Optional

This will generate a combined VCF called combined.vcf. Here ann_vcf is a way to annotate the respective VCF file in the info field with Annotation=FIRST. Note that varcomb does not compress the final VCF file. It is recommended the user does this:

$ bgzip combined.vcf
$ tabix combined.vcf.gz

which will also generate the index file combined.vcf.gz.tbi.