Quick Start

To help verify the installation and showing the workflow, we include a small data set and commands to genotype this simulated dataset. If you have already installed adVNTR, jump to Genotype Predefined VNTR in Simulated Data.

Install

The easiest way to get started is to Install adVNTR with conda. To install adVNTR, run these commands:

conda config --add channels bioconda
conda install advntr

Genotype Predefined VNTR in Simulated Data

To genotype a VNTR in the simulated dataset, one option is to use predefined models. Download vntr_data_recommended_loci.zip and extract it inside the project directory to use these models from human genome. Here, we genotype a VNTR with id 301645 that corresponds to a disease-linked VNTR. The list of some known VNTRs and their ID is available at Disease-linked-VNTRs page in wiki.

Then, download simulated sequencing data of a human sample. It only includes reads around a VNTR in CSTB gene which is known to be linked to progressive myoclonus epilepsies. Run this command to get 2/5 genotype for this VNTR.

advntr genotype --vntr_id 301645 --alignment_file CSTB_2_5_testdata.bam --working_directory working_dir

Genotype Custom VNTR

You can train a new model for a VNTR that doesn’t exist in predefined models. Instead of downloading vntr_data_recommended_loci.zip, you need the organism (here, human) reference genome to train a model for a specific VNTR. Download chromosome 21 of hg19 and extract it. It is recommended to have full reference genome of the organism to add the model, however, we use a single chromosome in quickstart since it is easier to download and runs faster. Run this command to add the VNTR in CSTB gene and train VNTR-specific scores:

advntr addmodel -r chr21.fa -p CGCGGGGCGGGG -s 45196324 -e 45196360 -c chr21

If you run the above command without using predefined models, this VNTR gets the first id. Run genotype command to get 2/5 genotype:

advntr genotype --vntr_id 1 --alignment_file CSTB_2_5_testdata.bam --working_directory working_dir