text: user174: I downloaded a VCF file from dbSNP, and I'm curious if the indels in the file are left-aligned for GRCH37 genome. The documentation doesn't say anything.
  How can we tell if a VCF file has left or right aligned indels?
  
  user964: By definition in the VCF format specification the POS field is left aligned 
  
  POS int32 t 0-based leftmost coordinate
  
  To confirm that you VCF is following the standard you would have to look at the reference and the match up the entries in the VCF.  However if it is from a reliable source like dbSNP you can probably assume they follow the spec 
  
  user1310: One possibility is to run bcftools norm on the file. At the end it will print out a statistic about how many variants were realigned. I did this for dbSNPv151 (GRCh38) only for chromosome 22 like this:
  $ bcftools view -i 'TYPE="indel"' dbSNP_GRCh38.p7_b151.vcf.gz 22|bcftools norm -Ou -f GRCh38.fa > /dev/null
  Lines   total/split/realigned/skipped:  901503/0/490/0
  
  
original_text: 174: <p>I downloaded a VCF file from dbSNP, and I'm curious if the indels in the file are left-aligned for GRCH37 genome. The documentation doesn't say anything.</p>
  
  <p>How can we tell if a VCF file has left or right aligned indels?</p>
   964: <p>By definition in the <a href="https://samtools.github.io/hts-specs/VCFv4.3.pdf" rel="noreferrer">VCF format specification</a> the POS field is left aligned </p>
  
  <blockquote>
    <p>POS int32 t 0-based leftmost coordinate</p>
  </blockquote>
  
  <p>To confirm that you VCF is following the standard you would have to look at the reference and the match up the entries in the VCF.  However if it is from a reliable source like dbSNP you can probably assume they follow the spec </p>
   1310: <p>One possibility is to run <a href="http://www.htslib.org/doc/bcftools.html#norm" rel="noreferrer">bcftools norm</a> on the file. At the end it will print out a statistic about how many variants were realigned. I did this for dbSNPv151 (GRCh38) only for chromosome 22 like this:</p>
  
  <pre><code>$ bcftools view -i 'TYPE="indel"' dbSNP_GRCh38.p7_b151.vcf.gz 22|bcftools norm -Ou -f GRCh38.fa &gt; /dev/null
  Lines   total/split/realigned/skipped:  901503/0/490/0
  </code></pre>
  