Hi Mohammed,

It depends a bit how techno-savvy you are. Harald makes a great suggestion but most non-computer people may struggle. If you're not computationally inclined, I'd suggest annotating your vcf files with SeattleSeq online: http://snp.gs.washington.edu/SeattleSeqAnnotation138/

That will give you a good idea of coding variants, SNPs, population prevalences etc. From that annotated file, you should be able to derive a list of variants that are rare and potentially family specific. The list is likely to contain hundreds to thousands of variants but would be easy to compare the two lists in excel.

But bear in mind that the mutation calling that resulted in your vcf files is somewhat error prone and a missing call in one sample doesn't totally rule out its presence in the other sample.

You might want to try this:

http://www.gene-talk.de/

The ```vcftools --diff --diff-site``` option would work for your specific case, which is what Harald was referring to.

To mention other options, bcftools is supposedly faster at this, and if you use bcftools what you want is the intersection function, isec. On mac or Linux with bcftools installed, you could use something like the following (where $ is the command line prompt) to get the list of SNPs at the intersection of two or more VCF files:

```

$ bcftools isec -n +2 file1.vcf.gz file2.vcf.gz | bgzip -c > isec_file1-v-2_out.vcf.gz

```

If you wanted just statistics on the numbers of SNPs in common between files, you could use the ```vcf-compare``` tool that comes with vcftools. See the documentation (http://vcftools.sourceforge.net/perl_module.html#vcf-compare).