Try vcftools. You will have to use tabix and bgzip that comes with tabix. These tools are basically for compressing and indexing the vcf file. It has to be done beofre using vcf tools.

I wrote a tool named vcf2sqlite: it put one ore more VCFs into a local sqlite3 database. The schema is simple and you can query the database using some simple SQL statements.

$ sqlite3 -column -header  db.sqlite \
   "select SAMPLE.name,VCFCALL.value,count(*) from VCFCALL,SAMPLE where SAMPLE.id=VCFCALL.sample_id and prop='GT' group by SAMPLE.id,VCFCALL.value"

name         value       count(*)  
-----------  ----------  ----------
rmdup_1.bam  0/1         545       
rmdup_1.bam  1/1         429       
rmdup_2.bam  0/1         625       
rmdup_2.bam  1/1         349       
rmdup_3.bam  0/1         595       
rmdup_3.bam  1/1         379       
rmdup_4.bam  0/1         548       
rmdup_4.bam  1/1         426       
rmdup_5.bam  0/1         564       
rmdup_5.bam  1/1         410       
rmdup_6.bam  0/1         724       
rmdup_6.bam  1/1         250