I want to filter the wild-type genotype in the cell lines. If the gene has no protein_change or var_annotation, does it mean the cell line is wild type for that gene? Thanks.
Likely, but I wouldn’t say that it’s guaranteed to be wild type. It’s possible that we might not have sequencing coverage for the gene. Also, another edge case I’ve heard of: we filter out germ line mutations, so common variation (such as in BRCA) is not reported.
We’ve had some discussions around this internally, and while we recognize the value of having WT calls for genes for use in analysis, but we don’t presently make those calls.