text: user2141: Currently, I am working on NGS data and my aim is to get significance prediction of variants present in the vcf file. As we know about SIFT Score for significance score prediction, I am trying to understand how this score works. When I read its reference paper, in the method section, the procedure to determine the sift score starts with patient protein query sequence. 
  My question is how to get patient protein sequence from patient data (either vcf file or bam file) (which is not explained in the paper). Rest I can follow by other algorithms like PSI-BLAST & MOTIF.
  Any suggestions....
  Thanks
  
  user939: You can use SIFT in two different ways. One way is manually via their website. This is done by downloading the protein sequence (fasta) from a reliable repository (e.g., uniprot or NCBI), and change the amino acid of interest. Then calculate the SIFT score.
  The other way, which is probably what you are interested in is with NGS data. Here normally SIFT is already known (precalculated) for all coding SNPs, and you can use that info directly during annotation of your variants. I don't know which variant annotation pipeline you are using, but for example annovar has SIFT data available at their databases repository.
  
  user1332: Ensembl now have a tool called Haplosaurus (still in beta) which will convert your phased VCF into actual protein sequences. 
  
  Haplosaurus
  haplo is a local tool implementation of the same functionality that
    powers the Ensembl transcript haplotypes view. It takes phased
    genotypes from a VCF and constructs a pair of haplotype sequences for
    each overlapped transcript; these sequences are also translated into
    predicted protein haplotype sequences. Each variant haplotype sequence
    is aligned and compared to the reference, and an HGVS-like name is
    constructed representing its differences to the reference.
  This approach offers an advantage over VEP's analysis, which treats
    each input variant independently. By considering the combined change
    contributed by all the variant alleles across a transcript, the
    compound effects the variants may have are correctly accounted for.
  haplo shares much of the same command line functionality with vep, and
    can use VEP caches, Ensembl databases, GFF and GTF files as sources of
    transcript data; all vep command line flags relating to this
    functionality work the same with haplo.
  Usage
  Input data must be a VCF containing phased genotype data for at
    least one individual; no other formats are currently supported.
  When using a VEP cache as the source of transcript annotation, the
    first time you run haplo with a particular cache it will spend some
    time scanning transcript locations in the cache.
  ./haplo -i input.vcf -o out.txt -cache
  
  
  
original_text: 2141: <p>Currently, I am working on NGS data and my aim is to get significance prediction of variants present in the vcf file. As we know about <a href="http://sift.jcvi.org/" rel="nofollow noreferrer">SIFT Score</a> for significance score prediction, I am trying to understand how this score works. When I read its <a href="http://sift.jcvi.org/" rel="nofollow noreferrer">reference paper</a>, in the method section, the procedure to determine the sift score starts with patient protein query sequence. </p>
  
  <p>My question is how to get patient protein sequence from patient data (either vcf file or bam file) (which is not explained in the paper). Rest I can follow by other algorithms like PSI-BLAST &amp; MOTIF.</p>
  
  <p>Any suggestions....</p>
  
  <p>Thanks</p>
   939: <p>You can use SIFT in two different ways. One way is manually via their website. This is done by downloading the protein sequence (fasta) from a reliable repository (e.g., uniprot or NCBI), and change the amino acid of interest. Then calculate the SIFT score.</p>
  
  <p>The other way, which is probably what you are interested in is with NGS data. Here normally SIFT is already known (precalculated) for all coding SNPs, and you can use that info directly during annotation of your variants. I don't know which variant annotation pipeline you are using, but for example annovar has SIFT data available at their <a href="http://annovar.openbioinformatics.org/en/latest/user-guide/download/" rel="nofollow noreferrer">databases</a> repository.</p>
   1332: <p>Ensembl now have a tool called <a href="https://github.com/Ensembl/ensembl-vep#haplo" rel="nofollow noreferrer">Haplosaurus</a> (still in beta) which will convert your phased VCF into actual protein sequences. </p>
  
  <blockquote>
    <h2>Haplosaurus</h2>
    
    <p><code>haplo</code> is a local tool implementation of the same functionality that
    powers the Ensembl transcript haplotypes view. It takes phased
    genotypes from a VCF and constructs a pair of haplotype sequences for
    each overlapped transcript; these sequences are also translated into
    predicted protein haplotype sequences. Each variant haplotype sequence
    is aligned and compared to the reference, and an HGVS-like name is
    constructed representing its differences to the reference.</p>
    
    <p>This approach offers an advantage over VEP's analysis, which treats
    each input variant independently. By considering the combined change
    contributed by all the variant alleles across a transcript, the
    compound effects the variants may have are correctly accounted for.</p>
    
    <p><code>haplo</code> shares much of the same command line functionality with <code>vep</code>, and
    can use VEP caches, Ensembl databases, GFF and GTF files as sources of
    transcript data; all <code>vep</code> command line flags relating to this
    functionality work the same with <code>haplo</code>.</p>
    
    <h2>Usage</h2>
    
    <p>Input data must be a VCF containing phased genotype data for at
    least one individual; no other formats are currently supported.</p>
    
    <p>When using a VEP cache as the source of transcript annotation, the
    first time you run haplo with a particular cache it will spend some
    time scanning transcript locations in the cache.</p>
  
  <pre><code>./haplo -i input.vcf -o out.txt -cache
  </code></pre>
  </blockquote>
  