How to convert VCF format file into Fasta(.fa) with the Reference data I need a Software or Python Program for Converting VCF(.vcf) to  FASTA(.fa) format with the help of reference (.fa)
I used FastaAlternateReferenceMaker previously. You will need to download GATK first. Next you prepare your reference genome (reference.fasta) and your vcf file (input.vcf). You will call the GATK function like this:

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


output.fasta will contain the new fasta with snps inserted at sites specific by the vcf file