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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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All N's in MPX consensus #109

Closed DrB-S closed 2 years ago

DrB-S commented 2 years ago

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 commented 2 years ago

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

DrB-S commented 2 years ago

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

DrB-S commented 2 years ago

That was the problem.