How to properly interpret the ALT and QUAL fields in bcf file from bcftools mpileup
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3 months ago
gt • 0

Hi there, I'm pretty new to DNA-seq and I am having a tough time interpreting the ALT and QUAL fields of a bcf file. I have been searching online for a while to find a concise answer, but I am not finding anything. I am working with E.coli data. I would like to know

1) When the ALT field is <*> does this mean that I have a deletion at this position?

2) When the ALT field is <*> and the QUAL score is 0 does this mean that we are not confident in the deletion? I have been seeing conflicting information online about this

3) What does it mean if I have for instance A,<*> in the ALT field? That it could either be a deletion or a variant?

Would really appreciate any help here or even direction to a thorough explanation elsewhere. Thanks!

bcftools DNA-seq mpileup • 145 views

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