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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Path/allele were could not be traced #105

Closed mekkiboussaha closed 7 months ago

mekkiboussaha commented 12 months ago

Sorry to bother you with this issue, but I am kind of new in the field and there are things that I could not understand. I constructed the graph using 2 samples. Then I run gfatools to call SVs and finally I run "minigraph --call" to find the path/allele. in the output file for this last step, I observed something like this: 19 6215950 6216037 >s32400 >s32402 *:0:+:19:6011048:6011135 19 6232539 6232540 >s32402 >s32404 . What does the "." in the last column of the second result means exactly? Thank you very much for your help. Best regards

ASLeonard commented 11 months ago

Hey Mekki, The "." is effectively missing (same as VCF), there is a more detailed answer here #34.

mekkiboussaha commented 11 months ago

Hi Alex and thanks a lot for your clarification.

Regards

Mekki

Mekki BOUSSAHA, Computational Biologist, IRHC, HDR INRAE - UMR1313 GABI Equipe Génétique et Génomique Bovines 78350 Jouy-en-Josas - France Tel. : +33 1 34 65 26 46

De : Alex Leonard @.***> Envoyé : mardi 5 décembre 2023 15:18:58 À : lh3/minigraph Cc : Mekki Boussaha; Author Objet : Re: [lh3/minigraph] Path/allele were could not be traced (Issue #105)

Hey Mekki, The "." is effectively missing (same as VCF), there is a more detailed answer here #34https://github.com/lh3/minigraph/issues/34.

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lh3 commented 7 months ago

Thank you, @ASLeonard