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bcgsc / straglr

Tandem repeat expansion detection or genotyping from long-read alignments
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About quality of detected VNTRs #14

Closed Jesson-mark closed 2 years ago

Jesson-mark commented 2 years ago

Hi, @readmanchiu

I'm currently wondering how to assess the quality of tandem repeats detected by Straglr. Since Straglr can report number of support reads for each TR, I wonder if a threshold could be applied to filter TRs whose number of support reads are below this threshold. If so, could you give any suggestions about how to choose this threshold?

Thanks!

Jesson-mark

readmanchiu commented 2 years ago

You can use min_support to set the threshold. I usually set it to 5 for my work.

Jesson-mark commented 2 years ago

Thanks for your reply. I will have a try.