Hi,
I'm working on multi-sample variant calling using samtools. And I encountered a problem: what value should I set for the option 'm' in bcftools view.
Because at https://github.com/samtools/samtools/wiki/FAQ, it is said that samtools "Recent versions (tagged as 0.1.19 or newer) implement a new calling model (bcftools view -m) where multi-sample calling comes at no sensitivity cost. It also fixes some of the known issues with multiallelic sites. This is currently the recommended way of calling.". And I can not see a default value for 'm' when I simply type './samtools-0.1.19/bcftools/bcftools view'.
What value should I set for 'm', or just type '-m' with no argument?
Another small question is that if I could do multi-sample variant calling on individuals from different breeds but the same species using samtools?
Thanks!