bcftools mpileup giving more wildtypes <*> than expected
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3 months ago
gt • 0

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?

bcftools DNA-seq mpileup • 292 views
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3 months ago

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

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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.