How to manipulate a reference FASTA or bam to include variants from a VCF?
GATK has a solution that might work for you:
FastaAlternateReferenceMaker, which : "Given a variant callset, this tool replaces the reference bases at variation sites with the bases supplied in the corresponding callset records." 


  Input
  
  The reference, requested intervals, and any number of variant ROD files.
  
  Output
  
  A FASTA file representing the requested intervals.
  
  Usage example

java -jar GenomeAnalysisTK.jar \
   -T FastaAlternateReferenceMaker \
   -R reference.fasta \
   -o output.fasta \
   -L input.intervals \
   -V input.vcf \