Yan Gao

I am running it on both bam files. Not finished on all datasets yet, but based on truvari, the two vcf files are very similar. Will update the final result...

Hi, just want to update that: across different coverage 15~40X, and on both hifi and ONT data, the precision/recall of raw and smooth.bam are all very similar. One side quesion:...

Here are the truvari result for 15X: ``` cat ../../15X/svdss/svdss.Truvari_v5.3/refine.variant_summary.json { "TP-base": 24502, "TP-comp": 23314, "FP": 2215, "FN": 3686, "precision": 0.9132359277684202, "recall": 0.8692351355186604, "f1": 0.890692445767286, "base cnt": 28188, "comp cnt":...

I am using ONT R10 datasets: HG002_PAW70337, 2025-01, probably the latest datasets. For HiFi 15X: ``` cat 15X/svdss/svdss.Truvari_v5.3/refine.variant_summary.json { "TP-base": 23291, "TP-comp": 21436, "FP": 928, "FN": 4897, "precision": 0.9585047397603291, "recall":...

The parameters are fine. I think this is a bug related to the banding part. I will try to fix it this week. For your example data, I see this...

A quick fix (add820b) was pushed, although I am not sure how this overflow happens yet. Let me know if this passes the test or not.

The difference comes from two reasons: 1) you used seeding and progressive tree to order the input sequence, which does not work well for this repeat region sequences. I did...

But I do agree that they are not real optimal alignment results. It may not be easy, but I will try to improve it.

The difference between different strands is because abpoa always puts gaps in the left-most position. To get the same result, gaps should be put on the right side for the...

Hi @glennhickey again, I am adding a parameter for abpoa to deal with this type of homopolymer sequence alignment to reach better visual alignment results. I also encountered this type...