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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Add support for proximal inframe indels #757

Open susannasiebert opened 2 years ago

susannasiebert commented 2 years ago

With #754 we're halfway to also supporting inframe indels so we should just do the rest of the work necessary to support those types of proximal variants.

malachig commented 1 year ago

Note to self. It would also be awesome to also support proximal frameshift indels. When we see these, they are generally somatic not germline. Often when one examines these carefully they usually look like a complex variant (one variant called a missense SNV, another a frameshift indel). The AA change predictions for both individual variants may be wrong and one of the time consuming elements of genomic review of candidates is manually correcting these variants to predict the correct peptide and performing neoantigen analysis on these corrected sequences.