Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis. The wrapper is thought of as a "run and forget" program. It abstracts away the complexity of the pre.py requirements for VCF files and provides a simple interface for preprocessing any VCF file.
It requires Python 3 and the Pysam package. However, it is also containerized in Docker and Singularity, so it can be used out of the box without any installation.
We recommend using singularity-ce with a version higher than 3.9.0. You can download the Singularity container using the following command (does not require root privileges):
singularity pull prepy-wrapper.sif oras://ghcr.io/eucancan/prepy-wrapper:latest
If you want to build the container yourself, you can use the singularity.def file (requires root privileges):
sudo singularity build --force prepy-wrapper.sif singularity.def
You can download the Docker image using the following command:
docker pull ghcr.io/eucancan/prepy-wrapper:latest
You can build the Docker container with the following command (requires root privileges):
docker build -t prepy-wrapper .
Check the example folder for an example of how to use the wrapper and the bulk wrapper.
The bulk wrapper's interface is the following:
usage: bulk.py [-h] -i INPUT_DIR -o OUTPUT_DIR -f FASTA_REF [-p PROCESSES]
options:
-h, --help show this help message and exit
-i INPUT_DIR, --input-dir INPUT_DIR
Path to input directory
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
Path to output directory
-f FASTA_REF, --fasta-ref FASTA_REF
Path to reference FASTA file
-p PROCESSES, --processes PROCESSES
Number of processes
The basic usage is:
python3 bulk.py -i <input_dir> -o <output_dir> -f <reference_fasta>
It creates a structure of subfolders in <output_dir> with the same structure as <input_dir>, but with the normalized VCF files in each subfolder. If using the Singularity image, the command would be:
singularity exec <singularity_args> prepy-wrapper.sif python3 /opt/prepy-wrapper/src/bulk.py -i <input_dir> -o <output_dir> -f <reference_fasta>
See the Wrapper section for more information on the <singularity_args>.
The wrapper's interface is the following:
usage: Pre.py wrapper [-h] -i INPUT_VCFS [INPUT_VCFS ...] -f FASTA_REF -o OUTPUT_PREFIX [--keep_all] [--force]
options:
-h, --help show this help message and exit
-i INPUT_VCFS [INPUT_VCFS ...], --input_vcfs INPUT_VCFS [INPUT_VCFS ...]
Input VCF files
-f FASTA_REF, --fasta_ref FASTA_REF
Reference FASTA file
-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
Output prefix
--keep_all Keep all variants (including non-PASS)
--force Force overwrite of output files
The basic usage is:
python3 prepy-wrapper.py -i <input_files> -o <output_prefix> -f <reference_fasta>
If using the Singularity image, the command would be:
singularity exec <singularity_args> prepy-wrapper.sif python3 /opt/prepy-wrapper/src/prepy-wrapper.py -i <input_files> -o <output_prefix> -f <reference_fasta>
Note: For <singularity_args> we highly recommend using the -c or -e parameters along with --workdir, --bind and -H to avoid any issues with the execution of the singularity image. For example (assuming all files are within the current directory):
mkdir -p workdir
singularity exec -c --workdir $PWD/workdir --bind $PWD -H $PWD prepy-wrapper.sif python3 /opt/prepy-wrapper/src/prepy-wrapper.py -i <input_files> -o <output_prefix> -f <reference_fasta>
rm -rf workdir
The output of the wrapper is a normalized VCF file for each input VCF file. The output files are located in <output_prefix><input_file_basename>.normalized.vcf.gz. If there are variants that could not be normalized (SVs or CNVs), they are located in <output_prefix><input_file_basename>.skipped.vcf.
The dependencies are covered by their own respective licenses as follows:
- Python/Pysam package (MIT license)
Further dependencies (to be installed by the user of this software):
- Hap.py (Copyright (c) 2010-2015 Illumina, Inc.)