Requirements

Supported File Format

The variant-aware Cas-OFFinder tool supports the following file formats for processing and analysis.

• .vcf: Variant Call Format files, used for storing genomic variants

• .vcf.gz: Compressed VCF files, either .gz or bgzip VCF files.

Ensure your input file is in one of these formats for compatibility with the tool.

Required Tools for CLI and Local Deployment

For users who prefer to work via the command-line interface or deploy Variant-aware Cas-OFFinder locally, the following tools are required:

1. OpenCL device

2. bcftools: a utility for manipulating and filtering VCF files.

   • Create a conda environment

   conda create -n cas-offinder
   

   • install bcftools via conda:

     conda install -c bioconda bcftools
     

   • bcftools can be used to filter specific chromosomes.

   bcftools view -r chr6,chr10 Sample.vcf.gz -o Output.vcf.gz
   

3. tabix: A tool for indexing VCF files. It is used for fast random access to VCF files.

   • install tabix via conda:

   conda install -c bioconda tabix
   

   • For indexing a VCF file:

   tabix -p vcf Sample.vcf.gz