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sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file
http://sanger-pathogens.github.io/snp-sites/
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Warning: No SNPs were detected so there is nothing to output #96

Open pgcudahy opened 4 years ago

pgcudahy commented 4 years ago

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 commented 2 years ago

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.