--regions: a BED file containing regions to be used only in genome-scan

[minw2828]

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]

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.