eesiribloom
eesiribloom
if @mhjiang97 is using the --mosaic-include-germline tag will sniffles not report both SVs with AF 5-20% AND >20% ?
have you tried running with `--no-qc` option? It is probably being filtered out by sniffles for one reason or the other. If it crops up after that, I think it...
Is there a difference in basecalling with the same model e.g. [email protected] between dorado basecaller server and the standalone software?
this would be helpful
thanks for the reply @lfpaulin . If it's recommended that you use the copy number neutral state from the SNV data instead of the coverage would you recommend generating SNV...
@lfpaulin with inputting tumour SNVs would you recommend somatic SNV calls e.g. from clairS or regular "germline" SNVs from clair3 (assuming input from the same tumour bam in both)
modkit summary shows unexpected proportion of methylation - is my methylation information being lost
Hi @ArtRand that makes a lot of sense, I did wonder that myself. I ran `check-tags` and I can see one sample has an all context model and the other...
modkit summary shows unexpected proportion of methylation - is my methylation information being lost
Would it be helpful if there was a similar `--cpg` option with the `summary` and `sample-probs` commands as there is with `modkit pileup`?
Apologies for the duplication as I wasn't sure where the best place to get an answer was. The plots are generated from two samples of the same cancer type and...
I've tried running `modkit summary` on both samples For the R9.4.1 sample ``` > sampling 10042 reads from BAM > calculating threshold at 10(th) percentile > calculated thresholds: C: 0.640625...