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To find the shared SNPs between two different VCF files and exclude the SNPs found in a third, use VCF_Match.py:

./VCF_Match.py VCF_1 VCF_2 -r remove_VCF_3 > shared_SNPs.txt

To convert positions from one namespace to another with a delta file, use map_vcf.py:

./map_vcf.py shared_SNPs.txt delta_file

To weed out the SNPs that aren't within core regions, use in-core.py:

./in-core.py -i shared_SNPs.txt.map

Finally, to get the genes that these SNPs are in, use in-gene.pl:

perl in-gene.pl ref_file shared_SNPs.txt.map.core > genes.txt