<p>I have a number of VCF files, where each VCF file possesses variant data for a single patient (this is the way Illumina provides their data).  Is it possible to combine all of the data for the patients into one VCF file?  If so, how?  Can I use plink/seq to do this?!  </p>

<p>Any suggestions and leads would be extremely helpful.</p>

GATK *CombineVariants*, see:

- [CombineVariants - Combine variant records from different sources](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php)


From the above link usage examples:

Merge two separate callsets
 

    java -jar GenomeAnalysisTK.jar \
       -T CombineVariants \
       -R reference.fasta \
       --variant input1.vcf \
       --variant input2.vcf \
       -o output.vcf \
       -genotypeMergeOptions UNIQUIFY

 
Get the union of calls made on the same samples

     java -jar GenomeAnalysisTK.jar \
       -T CombineVariants \
       -R reference.fasta \
       --variant:foo input1.vcf \
       --variant:bar input2.vcf \
       -o output.vcf \
       -genotypeMergeOptions PRIORITIZE \
       -priority foo,bar