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estimated pass threshold with default settings very high (v0.5.0 and v.0.6.1)

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Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
45/100
Tipo di issue
Bug
Chiarezza
Abbastanza chiara
Stato di attività
Tranquilla
Stack tecnologico
rust
Ambito
bioinformatics, cli

Direzione di ricerca

Start with the modkit pileup and sample probs entry points using the default settings, reproducing the reported thresholds and comparing them with the documented lowest-10% behavior. Trace the threshold calculation from the logfile output and probability distributions; the issue is done when the threshold follows the intended percentile or the behavior and fix are clearly documented.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

troubleshooting

Hi!

I ran modkit pileup (v.0.5.0) on one of my ONT samples for 5mC and noticed that the pass threshold with the default settings was put very high. A lot of methylated calls were filtered out giving very low percentages. This is what the logfile shows:
estimated threshold too high 1, using 0.9941406

I also tried runnning it with the newer version (v0.6.1), but got the same issue. This is what the log file shows:
estimated threshold too high 1, using 0.9746094 (maximum explicit canonical probability)

I also ran the sample probs to see what the thresholds and distribution looks like. The threshold was the same as for the pileup for both versions, put at 1:
base percentile threshold
C 10 1
C 50 1
C 90 1

I understood from the documentation that with the default settings, the lowest 10% of probabilities are filtered out. But when i look at the probability distributions of this sample it does not seem to put the pass threshold at the 10th lowest percentile, but a lot higher (see attached picture)? This leads to the majority of data not passing the threshold and being filtered out.

For reference, all my ONT samples get the exact same threshold put. I've played around with the filter settings myself, but there is no best practice for what threshold to put it at (yet) so this is not the best option for me at this moment.

Could you tell me why this happens and how I could fix it?
Image

Lingua principale
Rust
Stelle
280
Fork
35
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