SnpEff filter PASS - what are the QC filters?

Question

[Jennifer]

One of the outputs of the SnpEff variant annotation tool is a column called "filter". According to the documentation, it represents "whether or not the variant passed quality filters". I've searched the documentation extensively for what is entailed by this quality filter, but there appears to be no explanation. Relatedly, I've also searched for how the column "quality score" is calculated, but can find no information in the documentation.

Does anybody know what are the quality filters applied to get a value of "filter == PASS", and how is the quality score calculated?

Answer 1

[Ram]

FILTER is from the variant caller, not the variant annotator. You should go back one step and look at the filter criteria passed to the caller.

[Jennifer]

Thank you!