repClass field in

[Arturo G.V.]

Dear UCSC Browser People,

I am working on a variant calling pipeline. In order to discard potential false positive calls, I thought of flagging or removing all calls in repetitive regions, so I downloaded the repeats track from http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/rmsk.txt.gz.

I find that in this track the repetitive elements are categorized by the repClass column. I was not able to find a description of how this annotation was performed or what each of the categories means, and it concerns me that I will be discarding true variants if applying this filter without discriminating on the basis of repClass.

More particularly, I would like to know what the DNA and RNA classes are.

Thank you.

Arturo

[Luis Nassar]

Hello, Arturo.

Thank you for your interest in the Genome Browser.

That file corresponds to our RepeatMasker track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=rmsk). On the description page there is additional information on how the data were generated, and the different classes (including DNA/RNA classes).

Let us know if you have any further questions on this data on anything else we can help with.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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