afrubin
commented
1 month ago @ashsny This came up again when talking with folks at Wellcome Sanger, who have sequenced their HAP1 line and have found that it has alterations in sequences that are part of the mutational scan.
Since we want to handle SGE data by using a reference transcript, it's going to be important to be able to provide information about background mutations that affect every variant.
There's a straightforward solution that doesn't require any new features where we just make every variant a multi-mutant, but I think that is clumsy and will make integrating the data later on very cumbersome.
There might be other better ways to handle this and we can discuss options if you want.
Users may want to specify genetic changes that are relevant to a MAVE (e.g. a haplotype with variation that's not at the mutagenized locus or a risk allele that's present in the cell line).
We can do this by extending our existing support for VRS objects, by allowing users to upload a set of VRS objects describing this variation to an experiment record.
This will also allow us to improve the utility of mapped variants, since we can provide VRS objects that include this genetic background variation along with the variant measured in the experiment.