Which tool is used to annotate mutations?
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, 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. “Hotspot” is not a label in Variant_annotation, but can be obtained from the isTCGAhotspot and isCOSMIChotspot columns.
Coloring mutations in portal visualizations
The portal colors mutations with the priority order of hotspot > damaging > other non-conserving > other conserving. For instance, if a gene in a cell line has both hotspot and damaging mutations, it will be colored as hotspot. Silent mutations are not colored. These mutation categories are defined below. An example of this coloring scheme can be found here and in the following legend:
The mutation dataset is also available to plot as 0 or 1 on an axis in data explorer in cases such as grouping by Mutation. Note that this uses a binarized defintion of mutation, which includes any “hotspot”, “damaging”, or “other non-conserving” mutation.
Hotspot
- Is a hotspot in TCGA
- Is a hotspot in COSMIC
- Is not silent
Damaging
- Start_Codon_SNP
- Start_Codon_Del
- Start_Codon_Ins
- Splice_Site
- Frame_Shift_Del
- Frame_Shift_Ins
- Nonsense_Mutation
- De_novo_Start_OutOfFrame
Other non-conserving
- Missense_Mutation
- In_Frame_Del
- In_Frame_Ins
- Nonstop_Mutation
- Stop_Codon_Del
- Stop_Codon_Ins
Other conserving
- 5’Flank
- Intron
- IGR
- 3’UTR
- 5’UTR
Silent
- Silent
