Closed tsneddon closed 7 months ago
It's a bit hard to decide due to strand bias, among the four Ts, four are on positive strand and none on negative strand.
OK, thanks, does Clair3 have a default cut-off to filter based on strand bias? If so, how do we override it?
Clair3 handles strand bias in its neural network, it does not use a hard filter. Our observation is that Clair3 loosens the cutoff when coverage is low but all other supports are good. However, extreme cases like having all reads on one strand are mostly filtered.
Thank you for the explanation!
Hi: We just ran Clair3 on our first human ONP long-read data. In comparing SNV calls that we identified in the same genome with Illumina short-reads, we found a missense variant that did not make it into the Clair3 vcf file:
Looking at the alignment in IGV, it seems like it should have been called:
Any thoughts on why it is not in the Clair3 output file? Thanks!