Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files

Hi,

I sincerely hope that I am not repeating an already answered question. I couldn’t find the answer to my exact problem.

I have three VCF files derived using bcftools (isec). Those three files contain similar variations compared to the reference sequence. End of the day, I have

• Three VCF files representing three varieties (include only the common variations)
• Reference FASTA file
• Annotation (gff3) file for reference.

What I want to do is extract variations found in;

1. Gene region
2. 100 bp from TSS/+1 and the stop codon

Please note this is a 5 MB region (not a whole-genome, so there are no chromosomes).

I appreciate it if someone can help me in this regard.
Thank you!