Dan Lu

**Thank you for making such a useful tool!!** We have multiple samples and each sample have multiple vcfs generated by different SV callers. Based on discussion in #95, we should...

Keep small number of BA.2 on the tree and not filtered by clock_filter

2

**Context** On a general, all-lineage tree, when we have only 1 focal BA.2 sample, which pulled in just a few contextual BA.2 samples, most BA.2 samples ended up in excluded_by_diagnostics.txt...

meaning of warning:cant use more than 65535 sites

4

When running `somalier extract` I got a warning message: `warning:cant use more than 65535 sites` What does this mean? Should we reduce the number of variants we feed into somalier?...

`conda install -c bioconda vcfkit` or `conda install -c bioconda vcfkit=0.1.6` gives the following error 

different results from ska2 0.3.2 and 0.3.6

2

I was trying to run the latest version 0.3.6 (from `conda install -c bioconda ska2` today) with our data and the results are different from 0.3.2. The command for all...