search

Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
94 stars 16 forks source link

Does Pisces recognize the base quality score from PacBio HiFi reads? #57

Open turningA opened 3 years ago

turningA commented 3 years ago

I do notice that in your source code you have the following setup: private const int MaxBaseQuality = 93;

It looks like it will tolerate the base quality until 93.

But I want to confirm with you: whether Pisces is able to recognize the base quality if it is higher than 41?

turningA commented 3 years ago

I capped the base quality to 41 and get the same variant calls.

tamsen commented 3 years ago

Hi,

Thanks for using Pisces!

By default, Pisces accepts all bases over Q20, with equal weight. (We tried other methods and saw no improvement to accuracy, it just slowed things down. The knobs for monkeying with that model are still exposed if anyone wants to try anything different). Generally speaking, the only time the differences in high-scoring base call Q scores make a difference to variant calls is when the stitcher or Gemini is trying to make a decision on how to stitch reads who have different mismatches or cigar string differences in the overlap region, in which case the higher scores take precedence.