I have multiple VCFs for single cell RNA seq data and I want to get peptide sequences from these files. I have searched and found out that we can annotate the VCF with Ensembl's VEP to get the amino acids/protein information. However, I am looking to get a fasta file as an output which can be used for downstream analysis. I found out that GATK's FastaAlternateReferenceMaker can be used to get a fasta file from VCF. 

Can I use the output VCF from VEP as an input to the FastaAlternateReferenceMaker to get the required fasta? I am not sure if I should pass the entire VCF as an input or just the protein information. Please help me get a better understanding of this procedure.
I found out that this can be done in the following way:

 1. Find the proteins in the mutations using Ensembl's VEP and sending the VCF files as an input. By doing so we will get several information as an output but we are interested in Ensembl’s VEP protein ID which starts with **ENSP.** (VEP output format provided here: [https://m.ensembl.org/info/docs/tools/vep/vep_formats.html#vcfout][1])
 2. Once we have the protein IDs we can use the REST API provided by Ensembl and pass the ID to get the fasta:
[https://rest.ensembl.org/sequence/id/ENSP00000404426?content-type=text/x-fasta;type=protein][2]


  [1]: https://m.ensembl.org/info/docs/tools/vep/vep_formats.html#vcfout
  [2]: https://rest.ensembl.org/sequence/id/ENSP00000404426?content-type=text/x-fasta;type=protein