How were CCLE SNPs annotated?

Question

[A. Domingues]

I am looking at some variants in The Cancer Cell Line Encyclopedia (CLLE), via the DepMap portal which have been annotated in as "splice site" and "damaging" for "Variant Classification" and Variant Annotation". However, I cannot find any information, either in the website or the 2019 paper of these annotations were created.

Does anyone know?

Answer 1

[A. Domingues]

Got the answer in the Forum of DepMap (closed access). I am pasting here the crucial part of the answer. If any one from DepMap has an issue with it, I am happy to remove it:

We use Oncotator to annotate the mutations. The output of this tool is stored in the ‘Variant_Classification’ column of the mutation maf file The Variant_annotation column in the CCLE_mutations.csv MAF file

We have added a Variant_annotation column in the DepMap mutation data, CCLE_mutations.csv 4, which groups mutations using more inclusive definitions. The Variant_annotation column labels a mutation as “damaging”, “other non-conserving”, “other conserving” or “silent” using the Variant_Classification column and the definitions below.