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Fase SNP genotyping tool for whole genome sequencing data and large SNP database.

Install from Bioconda

VarGeno can be installed from Bioconda with command conda install vargeno.

Go to this link for more information about Bioconda.

If you do not have Bioconda installed, you can install VarGeno from source code.

Quick Usage

VarGeno takes as input:

  1. A reference genome sequence in FASTA file format.
  2. A list of SNPs to be genotyped in VCF file format.
  3. Sequencing reads from the donor genome in FASTQ file format.

Before genotyping an individual, you must construct indices for the reference and SNP list using the following commands:

vargeno index ref.fa snp.vcf index_prefix

To perform the genotyping:

vargeno geno index_prefix reads.fq snp.vcf output_filename

Here index_prefix should be the same string as index generating.

Output format: VCF

VarGeno's genotyping results are in the "FORMAT" column of VCF file.

  1. genotypes: in "GT" field: 0/0, 0/1 or 1/1.
  2. genotype quality: in "GQ" field, encoded as a phred quality (Integer).

For details of "GT" and "GQ" fields, please refer to The Variant Call Format(VCF) Version 4.2 Specification.

Install from Source Code


  • A modern, C++11 ready compiler, such as g++ version 4.9 or higher.
  • The cmake build system (only necessary to install SDSL library. If SDSL library already installed, cmake is not needed)
  • A 64-bit operating system. Either Mac OS X or Linux are currently supported.

Install Command

git clone
cd vargeno
bash ./

You should then see vargeno in vargeno directory. To verify that your installation is correct, you can run the toy example below.


The example dataset is in .

In this example, we genotype 100 SNPs on human chromosome 22 with a small subset of 1000 Genome Project Illumina sequencing reads. The whole process should finish in around a minute and requries 34 GB RAM.

  1. go to test data directory

  2. pre-process the reference and SNP list to generate indices:

vargeno index chr22.fa snp.vcf test_prefix
  1. genotype variants:
vargeno geno test_prefix reads.fq snp.vcf genotyped.vcf

The expected output of VarGeno on the example dataset should be

Memory Lite Version

The memory lite version of VarGeno (VarGeno-Lite) is maintained as an independent project in


If you use VarGeno in your research, please cite

  • Chen Sun and Paul Medvedev, Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

VarGeno's algorithm is built on top of LAVA's. Its code is built on top of LAVA's and it reuses a lot of LAVA's code. It uses some code from the AllSome project.