Feature request: Add Gene or Region-Based Annotation using SnpSift Intervals

[berntpopp]

Description:
Enhance the annotation pipeline by integrating SnpSift intervals to provide gene or region-based annotations. This feature will allow users to annotate VCF files based on specific genomic intervals, such as genes or regions of interest.

Requirements:

1. Update configuration file:

   • Include parameters for SnpSift intervals, such as the intervals file path.

2. Add new Snakemake rule:

   • Create a rule to run SnpSift intervals on the annotated VCF files.
   • Example command:

     java -jar SnpSift.jar intervals -v intervals.bed input.vcf | bgzip -c > output.vcf.gz

3. Output:

   • Annotated VCF files with INFO fields based on specified genomic intervals.

4. Documentation:

   • Update the README to include new steps and usage instructions for the SnpSift intervals feature.