looking for a software to compare genotypes between VCF files?

[caswater]

Hi, I have a vcf for variants from a patient, and wish to compare the genotype calls against 1000 genome genotypes. So basically given a varnat whose genotype in the patient is AA, and I wish to ask among 1000 genome data, how many individuals bearing the same genotype. It would be best to list all the genotypes that are absent in the 1000 genome data.

Do you know any software can achieve this comparison?

Thank you very much.

[adaptivegenome]

I don't know of software that does that but I bet it would not be hard to script this...

[dawe]

Take a look to the latest SnpSift developments. It does not perform what you need directly, but it should be easy to perform what you want once you created a single VCF with multiple samples

[caswater]

thank you guys~ SNPsift is really good. I like it!!!!!

[krawitz]

Hi Caswater,
in GeneTalk's (www.gene-talk.de) vcfViewer you will see the number of individuals with the same genotype from the 1000 genomes and 5000 exomes project.
Is this what you were looking for?
best,
peter

[caswater]

Hi, Krawits

Your suggestion is awesome, and the software is exactly what I am looking for. I am now playing with it now ⋯⋯(^.^)