All N's in MPX consensus

[DrB-S]

Our local MPX sequence had all N's in it's consensus sequence, whereas a comparative SRR sequence did not. So a complete SNP matrix was not produced, though bcftools_variants ran successfully for both.

I therefore uncommented 3 lines in cecret.config to make sure ivar_consensus was working, but had the same results.

Do I need to use ivar_variants instead of bcftools_variants?

[erinyoung]

What depth are you using? 10X is likely enough if not using amplicon libraries.

[DrB-S]

That explains it! It was set to 100.
Thanks!

[DrB-S]

That was the problem.