TR region coordinates

[lixingii]

I want to ask whether the TR reference BED file used as input for TRGT is 0-based. If so, the reference allele in the output VCF will include one additional repeat unit. How will this affect the results, specifically the repeat copy number calculation for 1-bp TR?

[pbsena]

Hello,

The BED files are 0-based as per the BED definition. However, the VCF output does shift the coordinates by 1 and the prior bases are added by design. This is to comply with the VCF standard in case there is a full deletion of the tandem repeat, in which case the ALT would be just the base.

Hope that clarifies the confusion, and thank you for reporting, this should me made clear in our docs!