Non-reference expansion pathogenic alleles (LRS in particular)

[dnil]

Thank you @dnil,
This tool works very well. I'm trying to break down the results to avoid any misunderstandings.

I have the impression that the repeats bed file is the key to obtaining good results. Depending on the version of the pathogenic_repeats.hg38.TRGT.bed file used, there is not the same definition of patterns, and I think that this can lead to false negatives.
pathogenic_repeats.hg38.TRGT.bed:
chr16 66490398 66490453 ID=BEAN1;REASONS=TAAAA;STRUC=(TAAAA)n
chr16 66490398 66490467 ID=BEAN1;PATTERNS=TGGAA,TAAAA;STRUC=

And I was happy to have found an STR expansion in my index case, but the TAAAA pattern is not the one that is pathogenic in the literature, but (TGGAA)*TAAAA.

Mélanie

Originally posted by @mletexier-cnrgh in PacificBiosciences/trgt#45 (comment)

[dnil]

Again, thank you for the feedback.

Two things here: same order of motifs in reference files is absolutely required for correct pathogenic motif selection for the complex motifs.

But it is also a complication that STRanger only deals with the order of the motifs, not their content. This is a particular
issue for the non-reference expansions. Compare in particular RFC1. Most downstream users import the results and images into some graphical environment for evailuation anyway. This is something we have planned adding, any year now! 😄