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bcgsc / straglr

Tandem repeat expansion detection or genotyping from long-read alignments
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--regions: a BED file containing regions to be used only in genome-scan #47

Open minw2828 opened 2 months ago

minw2828 commented 2 months ago

Hello,

Thank you for developing the tool.

If I am expecting a repeat may or may not start with the --regions regions.bed, but will extend beyond the genomic regions that are defined within --regions regions.bed, would straglr be able to find it?

Many thanks, Min

readmanchiu commented 2 months ago

Yes, you can define your region to whatever you like. I would not recommend centromeric or regions densely populated with tandem repeats. Also by specifying --regions instructs Straglr to look for repeat expansions relative to the reference genome, it would not report sizing of all tandem repeats within the region if they are not expanded.