bcftools mpileup giving more wildtypes <*> than expected

Question

[gt]

Hi there, I am having trouble with interpreting bcftools mpileup vcf output. My file has almost all <*> listed for the alternate field.

I am aligning my paired-end reads to an E.coli reference genome. Anyone have any intuition as to why this is happening?

Answer 1

[Pierre Lindenbaum]

bcftools mpileup must be followed by bcftools call to call the variants. see "Variant calling" in http://www.htslib.org/workflow/

[gt]

Yep, I performed variant calling on the mpileup. I am just wondering why I have no ALT equal to "." in my vcf file at all. So when I call variants, my vcf file only has a very small number of mutations. I understand that "<*>" is a wild type but I would like to know if any of those could be possible indels.