Can a data file in VCF format be converted into FASTA?
You can try gatk function FastaAlternateReferenceMaker

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