text: user2033: Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants?
  For instance, rs4349859 is a known HLAB27 SNP.
  If I can find rs4349859 in the patient's VCF file, could I say he is HLAB27+ ?
  
  user37: Some papers claim that you can do HLA typing from exome sequencing data. I have not validated this myself. I also guess it depends on capture. Nonetheless, I don't think you can type HLA with VCF generated with a standard pipeline, which is not specifically designed for HLA. Current variant callers won't work on HLA genes due to their high diversity. Also in general, there are thousands of HLA-B alleles. In most cases, you can't find the allele by looking at only one SNP.
  No, you can't check if the patient has HLA-B27 only from VCF. There might be a hope if you get raw reads and run a proper HLA typing tool designed for such data.
  
original_text: 2033: <p>Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants?</p>
  
  <p>For instance, rs4349859 is a <a href="http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=6:31397510-31398510;source=dbSNP;v=rs4349859;vdb=variation;vf=2732890" rel="nofollow noreferrer">known</a> HLAB27 SNP.</p>
  
  <p>If I can find rs4349859 in the patient's VCF file, could I say he is HLAB27+ ?</p>
   37: <p>Some papers claim that you can do HLA typing from exome sequencing data. I have not validated this myself. I also guess it depends on capture. Nonetheless, I don't think you can type HLA with VCF generated with a standard pipeline, which is not specifically designed for HLA. Current variant callers won't work on HLA genes due to their high diversity. Also in general, there are thousands of HLA-B alleles. In most cases, you can't find the allele by looking at only one SNP.</p>
  
  <p>No, you can't check if the patient has HLA-B27 only from VCF. There might be a hope if you get raw reads and run a proper HLA typing tool designed for such data.</p>
  