text: user6249: I need a Software or Python Program for Converting VCF(.vcf) to  FASTA(.fa) format with the help of reference (.fa)
  
  user5077: 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
  
original_text: 6249: <p>I need a Software or Python Program for Converting VCF(.vcf) to  FASTA(.fa) format with the help of reference (.fa)</p>
   5077: <p>I used <a href="https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php" rel="nofollow noreferrer">FastaAlternateReferenceMaker</a> previously. You will need to download <a href="https://software.broadinstitute.org/gatk/download/" rel="nofollow noreferrer">GATK</a> first. Next you prepare your reference genome (reference.fasta) and your vcf file (input.vcf). You will call the GATK function like this:</p>
  
  <pre><code> java -jar GenomeAnalysisTK.jar \
     -T FastaAlternateReferenceMaker \
     -R reference.fasta \
     -o output.fasta \
     -V input.vcf \
  </code></pre>
  
  <p>output.fasta will contain the new fasta with snps inserted at sites specific by the vcf file</p>
  