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.
bcftools mpileup giving more wildtypes <*> than expected
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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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Pierre Lindenbaum
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