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
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$\begingroup$ Can you share a genome browser URL that shows CN? I can't seem to find any CN track on the UCSC genome browser $\endgroup$– Ram RSCommented Jun 6 at 15:57
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$\begingroup$ 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. $\endgroup$– terdon ♦Commented Jun 6 at 16:05
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2 Answers
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If you want databases of known CNVs, you can have a look at:
You can also use VarSome, 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:
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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.
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$\begingroup$ 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 ... $\endgroup$– M__ ♦Commented Jun 7 at 13:08