<p>Most likely yes, they are the same.</p>
<p>However, &quot;NCBI37&quot; is an odd/unusual notation, because it doesn't indicate the species (human / mouse). Assuming it's a human genome (based on you comparing it to <em>hg</em>19 rather than <em>mm</em>19, or something else), then the correct name for the NCBI reference should be GRCh37.</p>
<p>As it's a different name, we can only make guesses as to what the people who generated the VCF meant. You'll need to talk directly to them in order to be sure.</p>

CC BY-SA 4.0
2023-06-05T05:11:19.950Z
2023-06-05T05:11:19.950Z
gringer
<p><em>This question was also asked on <a href="https://www.biostars.org/p/9565378/" rel="nofollow noreferrer">Biostars</a></em></p>
<p>In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome.</p>
<p>The VCF is from a lab sequencing human genomes, and they're no longer able to be reached out to. I can't provide a link to NCBI37 because I don't know what it is and I can't find much information on it.</p>
<p>Relevant line from VCF:
&quot;##reference=NCBI37&quot;</p>
<p>Here is part of the VCF header:</p>
<pre><code>##fileformat=VCFv4.2
##source=apt-format-result:2.10.2
##reference=NCBI37
##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;Genotype&quot;&gt;
##contig=&lt;ID=1&gt;
##contig=&lt;ID=10&gt;
##contig=&lt;ID=11&gt;
##contig=&lt;ID=12&gt;
##contig=&lt;ID=19&gt; [omitted some chromosomes for brevity]
##contig=&lt;ID=2&gt;
##contig=&lt;ID=20&gt;
##contig=&lt;ID=MT&gt;
##contig=&lt;ID=X&gt;
##contig=&lt;ID=Y&gt;
</code></pre>

<vcf><genome><reference-genome><hg19>
Is a human genome file with reference as NCBI37 the same as hg19?
# Is a human genome file with reference as NCBI37 the same as hg19?

(Asked by: username_0 on 2023-06-03)

This question was also asked on Biostars
In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome.
The VCF is from a lab sequencing human genomes, and they're no longer able to be reached out to. I can't provide a link to NCBI37 because I don't know what it is and I can't find much information on it.
Relevant line from VCF:
"##reference=NCBI37"
Here is part of the VCF header:
##fileformat=VCFv4.2
##source=apt-format-result:2.10.2
##reference=NCBI37
##FORMAT=
##contig=
##contig=
##contig=
##contig=
##contig= [omitted some chromosomes for brevity]
##contig=
##contig=
##contig=
##contig=
##contig=

**Tags:** vcf, genome, reference-genome, hg19

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## 1 answers

### Answer by username_1 on 2023-06-05. Score: 1 | Accepted answer

Most likely yes, they are the same.

However, "NCBI37" is an odd/unusual notation, because it doesn't indicate the species (human / mouse). Assuming it's a human genome (based on you comparing it to *hg*19 rather than *mm*19, or something else), then the correct name for the NCBI reference should be GRCh37.

As it's a different name, we can only make guesses as to what the people who generated the VCF meant. You'll need to talk directly to them in order to be sure.


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