gene4mVCF

Introduction

gene4mVCF is a Python package that allows you to extract variant entries for specific genes or a list of genes from a VCF (Variant Call Format) file. It utilizes tools like bcftools, tabix, and Python libraries like pysam, pandas, pybedtools, tqdm, and gffutils to efficiently parse and extract variants.

Installation

You can install gene4mVCF via pip:

$ pip install gene4mVCF

After installation please download the four required bed files and place inside the folder /gene4mVCF
'hg19.ensGene.bed' --> https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ensGene.gtf.gz

'hg19.ncbiRefSeq.bed' --> https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ncbiRefSeq.gtf.gz

'hg38.ensGene.bed' --> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ensGene.gtf.gz

'hg38.ncbiRefSeq.bed'--> https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz

Usage

Extract variant entries for a specific gene or list of genes from a VCF file.
usage: $ gene4mVCF [-h] -i INPUT -g GENE [-r REFERENCE]

Needed arguments:
-i INPUT, --input INPUT, is bgzip compressed VCF file

-g GENE, --genes GENE, is either a Gene name, Ensembl gene ID, or path to a genelist file with *.txt extension

optional arguments:

-h, --help show this help message and exit

-r REFERENCE, --ref REFERENCE, is 37 or 38, based on the reference genome used for creating the VCF file

-f FEATURE, --feature FEATURE, is feature type(s) to filter for (e.g., exon, CDS, 5UTR, 3UTR, transcript)

Examples

Extract variants for a single gene using gene name: $ gene4mVCF -i input.vcf.gz -g EGFR

Extract variants for a single using ensembl gene id: $ gene4mVCF -i input.vcf.gz -g ENSG00000168878

Extract variants for multiple genes listed in a file: $ gene4mVCF -i input.vcf.gz -g acmg-genes.txt

For more options and details, refer to the help message.

Example showing extraction of variants of ACTB gene

input command

Output file in the tab-separated format

Support

For any issues or inquiries, please open an issue on the GitHub repository https://github.com/vkulaganathan/gene4mVCF

Installation

Installation via pip:

$ pip install gene4mVCF

current version='1.1.5'