Hi Clair3 Developers,

First of all, thank you very much for developing Clair3. This tool has been extremely helpful for my research.

While analyzing Nanopore sequencing samples with Clair3 using the default parameters, I noticed that some variants were not being called. As shown in the attached figure, I looked at the allele fractions for these sites, and some examples are 75%:25% and 79%:21%.

I am wondering if these variants were missed because the allele fraction is too low. Is the default threshold for calling heterozygous variants 30% or higher? I also tried setting --snp_min_af, but it did not seem to have any effect. Is there any other parameter that can be adjusted to change the allele fraction threshold? On IGV, these sites clearly appear to be heterozygous variants.

Thank you very much for your time and help.

Best regards,
Chih-Hung Hsieh