Stefano Giulieri

icon company University of Melbourne icon location Melbourne icon location Clinician-researcher, infectious diseases physician. Interested in Staphylococcus aureus genomics, within-host evolution, statistical genomics.

Results 5 comments of Stefano Giulieri

generate a variant table for dnds calculation

Hi @smb20200615, you can use `bcftools merge` to merge the vcf files of your isolates: `bcftools -m none -0 -O z ... > merged.vcf.gz` You can then either use the...

generate a variant table for dnds calculation

No, snippy-core doesn't provide details of the null-sites, because it uses a strict definition of core genome (0% gaps). You can use `bcftools merge` without the option `-0` (`--missing-to-ref`) so...

How to run the pipeline?

Hi, the pipeline is very easy to run if installed with conda. If you run `BacGWASim` without any argument, it will run the program with default parameters. You can easily...

How to run the pipeline?

You dont' need any input data. It is a simulator

Simulation based on user-defined reference genome or tree

Hi @luciagrami, I'm not aware that this issue has been adressed. I'm not sure this tool is actively mantained (last commit 3 years ago). I found another GWAS simulation tool...