Question about using Adotto TRs with TRGT and their impact on phasing in HiPhase

[Maille0]

Hi,

First of all, thank you for your work on TRGT, it's a really useful tool for analyzing tandem repeats from long-read data !

I have a question regarding the use of the Adotto catalog with TRGT. In our project, we were interested in certain TRs that are included in the Adotto catalog but not present in the default BED file provided in the TRGT documentation. To include them in our analysis, we manually added these TRs from the Adotto resource into our BED file and used that as input for TRGT.

However, when these additional TRs are used in combination with DeepVariant and Sawfish variant calls as input for HiPhase, we observed a significant drop in the number of phased variants, seemingly because of the overlap filter (PF: TR_OVERLAP) in HiPhase, which removes phasing information for variants overlapping a TR.

This leads us to wonder:

Has there been any filtering or curation of the Adotto TRs prior to selecting those included in the default TRGT BED file?

Could some of the TRs from Adotto be less well-defined or problematic for downstream phasing tools like HiPhase?

Would you recommend any particular filtering strategy for integrating Adotto TRs into a TRGT-compatible BED?

Thanks again for your time and for this powerful tool.

Best regards,

Grégoire Blavier

[egor-dolzhenko]

Hi Grégoire. Thank you for the question. Would you be open to re-running your analysis on a different repeat catalog to see if the results improve? If yes, could you please reach out to me by email?

Best wishes,
Egor