Warning: No SNPs were detected so there is nothing to output

[pgcudahy]

I've got a set of 972 Mtb isolates that I'm trying to run snp-sites -c -o on, but it fails with the error Warning: No SNPs were detected so there is nothing to output. However, it works with removing the -c flag. How can I try and figure out which isolates are causing problems?

[hkeward]

This seems to happen because the -c option removes any call across all samples where any of your samples has a non-ACTG at that position. This could be due to a true deletion at that site, an area of a particular sample that has not aligned to your reference (low depth? poor quality?), or a site with some other non-ACTG character. With a large number of samples, even a single sample missing a call at a position will result in that call being removed entirely when -c is used. With a large number of samples, you're probably just filtering out all sites because at least one sample has a non-ACTG for every site.