about the process method of adotto TR annotation file

PacificBiosciences / trgt

Tandem repeat genotyping and visualization from PacBio HiFi data

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about the process method of adotto TR annotation file #37

Closed WeiCSong closed 1 month ago

WeiCSong commented 2 months ago

Hi, the adotto paper (nat biotech 2024) mentioned a total of 1.7m TR loci in hg38, whereas the adotto_hg38 bed file in TRGT tutorial has about 0.9m rows, is there any preprocess and filter step between them? Thanks for your help!

egor-dolzhenko commented 2 months ago

Thanks for the question! In the paper describing TRGT we used an older version of the Adotto repeat catalog. Here is a link to the version 1.0 of the Adotto catalog from @ACEnglish adapted for TRGT by @mdanzi.