How to calculate Tajima'D or fixation indices (FST) using inStrain files?

MrOlm / inStrain

Bioinformatics program inStrain

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How to calculate Tajima'D or fixation indices (FST) using inStrain files? #177

Open ChenTianYi99 opened 3 months ago

ChenTianYi99 commented 3 months ago

Hi, i have been using inStrain to profile viral microdiversity. I may need to calculate Tajima'D or fixation indices (FST) between population microdiversity. So are there any suggestions to run the steps or just generate VCF files for other tools?

Looking forward to your reply. Thanks in advance.

MrOlm commented 3 months ago

Hi @ChenTianYi99 ,

Unfortunately I don't have any particular advice to help with this. You should be able to convert SNVs.txt into a VCF file, but I don't have any experience doing it. You could also try https://github.com/alexcritschristoph/soil_popgen which is an offshoot of inStrain that can calculate things like this.

Best, Matt