How to view the tandem repeats in the VCF file generated by Sniffles2? about sniffles HOT 5 CLOSED

Dear @RenqiuguoLi
just to avoid confusion: Sniffles is a SV caller and thus a bit different than a tandem repeat caller (e.g. TRGT). The bed file is just to control merging of SV to be more aggressive in these regions.

For visualization we are often using IGV or Samplot .

For Tandem repeats it depends what technology you used: ONT (STRGLR) Pacbio (TRGT) are what I would recommend.

Hope that helps.
Fritz

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@fritzsedlazeck
Hi Fritz!
Thank you so much for your quick response.
I am currently performing the STR/VNTR calling from ONT reads.
Based on your knowledge, Do you have tools recommandations other than STRGLR for this?
I am really thankful appreciate for your advice and
Thank you so much

ps: I am using STRGLR right now,

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Hi @RenqiuguoLi
We are also testing medaka for this. Seems to be better than strglr..
Good luck
Fritz

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@fritzsedlazeck
Thank you for your generous answer and this question is also in my concern right now.
I am also doing STR/TR calling right now.
I traced back to where are those two bed files:

Source for human_hs37d5.trf.bed: https://github.com/PacificBiosciences/pbsv/tree/master/annotations
Source for human_GRCh38_no_alt_analysis_set.trf.bed: https://github.com/PacificBiosciences/pbsv/tree/master/annotations

I was wondering what is can I feed these two to Straglr & medaka for STR/TR calling?
Do these two bed files contain global genes? and are they accreditable

from sniffles.

"
I was wondering if I could feed these two bed files into Straglr & medaka for STR/TR calling?
Do these two bed files contain global genes? and are they accreditable?
"
Sorry for the typo

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