Need help understanding core SNPs

Question

[ujichu]

why cant i delete this post

[LauferVA]

surely on some level - new to bioinformatics or not - you must understand 2 things:

1) it is not possible to answer your question based on this post, which provides essentially none of the details necessary

2) being rude to one of the most prolific moderators on this site will get you no where.

[ujichu]

word count

[Prash]

Dear Ujichu

I was wondering whether the quality of your third isolate is in tact! You could use --minqual threshold. It may also be likely that the reads covered at a particular window/site is less than 10, the default being 10.

Pl try checking the quality and proceed

Best prash

[Pierre Lindenbaum]

https://github.com/tseemann/snippy : "Rapid haploid variant calling and core genome alignment"

[ujichu]

word count

[Pierre Lindenbaum]

I just wrote the link to help people identify the software (it's not a common tool I think)