Introduction¶
This package is aimed at providing a way of retrieving variant information using ANNOVAR and myvariant.info. In particular, it is suited for bioinformaticians interested in aggregating variant information into a single NoSQL database (MongoDB solely at the moment).
Installation¶
Ancillary Libraries¶
VAPr relies on a variety of packages to function correctly. Below are packages and dependencies required to ensure that VAPr works correctly.
Note
Jupyter, Pandas, and other ancillary libraries are not installed with VAPr and must be installed separately. These can be conveniently install using Anaconda:
$ conda install python=3 pandas mongodb pymongo jupyter notebook
MongoDB¶
VAPr is written in Python and stores variant annotations in NoSQL database, using a locally-installed instance of MongoDB. Installation instructions
BCFtools¶
BCFtools will be used for VCF file merging between samples. To download and install:
$ wget https://github.com/samtools/bcftools/releases/download/1.6/bcftools-1.6.tar.bz2
$ tar -vxjf bcftools-1.6.tar.bz2
$ cd bcftools-1.6
$ make
$ make install
$ export PATH=/where/to/install/bin:$PATH
Refer here for installation debugging.
Tabix¶
Tabix and bgzip binaries are available through the HTSlib project:
$ wget https://github.com/samtools/htslib/releases/download/1.6/htslib-1.6.tar.bz2
$ tar -vxjf htslib-1.6.tar.bz2
$ cd htslib-1.6
$ make
$ make install
$ export PATH=/where/to/install/bin:$PATH
Refer here for installation debugging.
ANNOVAR¶
(It is possible to proceed without installing ANNOVAR. Variants will only be annotated with MyVariant.info. In that case, users can skip the next steps and go straight to the section Known Variant Annotation and Storage)
Users who wish to annotate novel variants will also need to have a local installation of the popular command-line software ANNOVAR(1), which VAPr wraps with a Python interface. If you use ANNOVAR’s functionality through VAPr, please remember to cite the ANNOVAR publication (see #1 in Citations)!
The base ANNOVAR program must be installed by each user individually, since its license agreement does not permit redistribution. Please visit the ANNOVAR download form here, ensure that you meet the requirements for a free license, and fill out the required form. You will then receive an email providing a link to the latest ANNOVAR release file. Download this file (which will usually have a name like annovar.latest.tar.gz) and place it in the location on your machine in which you would like the ANNOVAR program and its data to be installed–the entire disk size of the databases will be around 25 GB, so make sure you have such space available!
Annotation Quickstart using ANNOVAR¶
An annotation project can be started by providing the API with a small set of information and then running the core methods provided to spawn annotation jobs. This is done in the following manner:
# Import core module
from VAPr import vapr_core
import os
# Start by specifying the project information
IN_PATH = "/path/to/vcf"
OUT_PATH = "/path/to/out"
ANNOVAR_PATH = "/path/to/annovar"
MONGODB = 'VariantDatabase'
COLLECTION = 'Cancer'
annotator = vapr_core.VaprAnnotator(input_dir=IN_PATH,
output_dir=OUT_PATH,
mongo_db_name=MONGODB,
mongo_collection_name=COLLECTION,
build_ver='hg19',
vcfs_gzipped=False,
annovar_install_path=ANNOVAR_PATH)
annotator.download_databases()
dataset = annotator.annotate(num_processes=8)
Downloading the ANNOVAR databases¶
If you plan to use Annovar, the command below will download the necessary Annovar databases. The code above includes this step. When Annovar is first installed, it does not install databases by default. The vapr_core has a method download_annovar_databases() that will download the necessary annovar databases. If you do not plan on using Annovar, you should not run this command. Note: this command only needs to be run once, the first time you use VAPr.
annotator.download_databases()
This will download the required databases from ANNOVAR for annotation and will kickstart the annotation process, storing the variants in MongoDB.