<p>If you want databases of known CNVs, you can have a look at:</p>
<ul>
<li><a href="http://dgv.tcag.ca/dgv/app/home" rel="nofollow noreferrer">Database of Genomic Variants</a> (DGV)</li>
<li><a href="https://www.deciphergenomics.org/" rel="nofollow noreferrer">DECIPHER</a></li>
<li><a href="https://commonfund.nih.gov/GTEx" rel="nofollow noreferrer">NIH GTEx</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/clinvar/" rel="nofollow noreferrer">Clinvar CNV</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/dbvar" rel="nofollow noreferrer">NCBI dbVar</a></li>
</ul>
<p>You can also use <a href="https://varsome.com/" rel="nofollow noreferrer">VarSome</a>, a free genomic variant search engine developed by the company I work for, which (among other things) shows structural variants from all of the sources above in a single genome browser. Click on the &quot;Structural Variants&quot; card, and then:</p>
<p><a href="https://i.sstatic.net/oJw4GlCA.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/oJw4GlCA.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2024-06-07T10:56:40.643Z
2024-06-07T10:56:40.643Z
terdon
<p>Thanks for all the responses,</p>
<p>I found one database that caters standard CNVs of hg38 as well as other versions. Although, I've to confirm which dataset will going to work for me. Please let me know if anyone has better thoughts or suggestions.</p>
<p><a href="http://dgv.tcag.ca/dgv/app/downloads?ref=GRCh37/hg19" rel="nofollow noreferrer">http://dgv.tcag.ca/dgv/app/downloads?ref=GRCh37/hg19</a></p>

CC BY-SA 4.0
2024-06-07T13:08:12.713Z
I'd look at NCBI's resources first as recommended by @terdon. This will provide the basis for further comparisons, such as Varsome, NIH, TCAG etc ...
M__
CC BY-SA 4.0
2024-06-06T18:11:26.140Z
2024-06-06T18:20:11.773Z
2024-06-06T18:20:11.773Z
Deb
<p>I'm wondering how can I get standard hg38 Copy number Variation (CNV) file from UCSC website.</p>
<p>Although, I got a link that is not working: <a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/wgEncodeCnvGtapLatest.bed.gz" rel="nofollow noreferrer">http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/wgEncodeCnvGtapLatest.bed.gz</a></p>

CC BY-SA 4.0
2024-06-06T15:57:52.003Z
Can you share a genome browser URL that shows CN? I can't seem to find any CN track on the UCSC genome browser
Ram RS
CC BY-SA 4.0
2024-06-06T16:05:58.990Z
What does "standard hg38 Copy number Variation" mean? What exactly are you expecting? Frequencies of known CNVs in the population? A list of known human CNVs? Rare CNVs that are actually present in the reference genome? Please [edit] your question and clarify.
terdon
<human-genome><ucsc><ncbi><copy-number>
Where can I get hg38 Copy number Variation (CNV) file?
# Where can I get hg38 Copy number Variation (CNV) file?

(Asked by: username_0 on 2024-06-06)

I'm wondering how can I get standard hg38 Copy number Variation (CNV) file from UCSC website.

Although, I got a link that is not working: <http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/wgEncodeCnvGtapLatest.bed.gz>

**Tags:** human-genome, ucsc, ncbi, copy-number
> **Comments:**
> **username_1**: Can you share a genome browser URL that shows CN? I can't seem to find any CN track on the UCSC genome browser  
> **username_2**: What does "standard hg38 Copy number Variation" mean? What exactly are you expecting? Frequencies of known CNVs in the population? A list of known human CNVs? Rare CNVs that are actually present in the reference genome? Please [edit] your question and clarify.  

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## 2 answers

### Answer by username_2 on 2024-06-07. Score: 3

If you want databases of known CNVs, you can have a look at:

* [Database of Genomic Variants](http://dgv.tcag.ca/dgv/app/home) (DGV)
* [DECIPHER](https://www.deciphergenomics.org/)
* [NIH GTEx](https://commonfund.nih.gov/GTEx)
* [Clinvar CNV](https://www.ncbi.nlm.nih.gov/clinvar/)
* [NCBI dbVar](https://www.ncbi.nlm.nih.gov/dbvar)

You can also use [VarSome](https://varsome.com/), a free genomic variant search engine developed by the company I work for, which (among other things) shows structural variants from all of the sources above in a single genome browser. Click on the "Structural Variants" card, and then:

[![enter image description here](https://i.sstatic.net/oJw4GlCA.png)](https://i.sstatic.net/oJw4GlCA.png)


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### Answer by username_0 on 2024-06-06. Score: 1

Thanks for all the responses,

I found one database that caters standard CNVs of hg38 as well as other versions. Although, I've to confirm which dataset will going to work for me. Please let me know if anyone has better thoughts or suggestions.

<http://dgv.tcag.ca/dgv/app/downloads?ref=GRCh37/hg19>

> **Comments:**
> **username_3**: I'd look at NCBI's resources first as recommended by @terdon. This will provide the basis for further comparisons, such as Varsome, NIH, TCAG etc ...  

---

