Installation

In order to use adVNTR, it is recommended to (1) install adVNTR using conda packaging manager and (2) download the predefined models for human genome from Data Requirements section. However, you can install it from the source and/or use custom models.

Install adVNTR with conda

If you are using the conda packaging manager (e.g. miniconda or anaconda), you can install adVNTR from the bioconda channel:

conda config --add channels bioconda
conda install advntr

adVNTR could be invoked from command line with advntr

Data Requirements

In order to genotype VNTRs, you need to either train models for loci of interest or use pre-trained models (recommended): * To run adVNTR on trained VNTR models:

• Download vntr_data_recommended_loci.zip and extract it inside the project directory. This includes a set of pre-trained VNTR models for Illumina (6719 loci) and Pacbio (8960 loci) sequencing data.
• You can also download and use vntr_data_genic_loci.zip for 158522 VNTRs that results in having much longer running time.

Alternatively, you can add model for custom VNTR. See Add Custom VNTR for more information about training models for custom VNTRs.

Execution:

Use following command to see the help for running the tool.

advntr --help

The program outputs the RU count genotypes of VNTRs. To specify a single VNTR by its ID use --vntr_id <id> option. The list of some known VNTRs and their ID is available at Disease-linked-VNTRs page in wiki.

See the demo execution here or Quick Start page to see an example data set with step-by-step genotyping commands.

Demo: input in BAM format

• --alignment_file specifies the alignment file containing mapped and unmapped reads:

advntr genotype --alignment_file aligned_illumina_reads.bam --working_directory ./log_dir/

• With --pacbio, adVNTR assumes the alignment file contains PacBio sequencing data:

advntr genotype --alignment_file aligned_pacbio_reads.bam --working_directory ./log_dir/ --pacbio

• Use --frameshift to find the possible frameshifts in VNTR:

advntr genotype --alignment_file aligned_illumina_reads.bam --working_directory ./log_dir/ --frameshift

Install from source (Not recommended)

You can also install adVNTR from the source instead of using conda. First, you need to install the following packages:

Dependencies

1. Following libraries are required to be installed on the system:

   • python2.7
   • python-pip
   • python-tk
   • libz-dev
   • samtools
   • muscle

You can install these requirement in Ubuntu Linux by running sudo apt-get install python2.7 python-pip python-tk libz-dev samtools muscle To install these packages on Mac OS, you can use Homebrew.

2. Following python2.7 packages are required:

   • biopython
   • pysam version 0.9.1.4 or above
   • cython
   • networkx version 1.11
   • scipy
   • joblib
   • scikit-learn

You can install required python libraries by running pip install -r requirements.txt

To Install

To get the latest version and install it locally, run:

git clone https://github.com/mehrdadbakhtiari/adVNTR
cd adVNTR
make; make install
python setup.py install

adVNTR could be invoked from command line with advntr