pab2025_Assignment02

Program description:

• The program is a Variant Density Calculator (VDC) Takes as Input (matching files):
• GFF (feature info.)
• VCF (variant info.) Outputs:
• Variant Density Calculation YAML formatted file
• Filtered VCF file containing only variants with selected features (e.g., exon,CDS)

Program structure:

• One file only program (vdc.py)

Program usage:

Needs to be run in a SHELL: Example:

• python vdc.py -gff {gff_file} -vcf {vcf_file} -var {vcf} -rep {yaml_file} -ftr exon,CDS

Requirements:

• Python with Python Standard Library