Fredrik Dyrkell

Thanks -- that did indeed seem to solve it! In my previous attempts I seem to have mixed up the `-L` parameter with `--ctg-min-length`.

Hello, Could this behaviour come from the early bail-out on https://github.com/tseemann/snippy/blob/master/bin/snippy-core#L282 That would be consistent with the described behaviour if all samples (for my $id (@id) loop) have $alt ==...

I think I managed to create a small(-ish) test case to verify this behaviour. See the attached file with the data (public data off of ENA/EBI) ``` $ snippy --version...

Sure! (I was able to download the testdata.zip, from my comment, I'm not sure if it's only available for myself?). Here's the result: ``` $ samtools faidx 148/snps.aligned.fa $ samtools...