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!