Frequently Asked Questions
So which one should I use?
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.
The mutation dataset is also available to plot as 0 or 1 on an axis in data explorer. Note that this uses a binarized defintion of mutation, which includes any "hotspot", "damaging", or "other non-conserving" mutation.
- Is a hotspot in TCGA
- Is a hotspot in COSMIC
- Is not silent
|Copy Number||hg19||hg19||hg19||hg38 lift||hg38|
The transition is now complete, and alignment for 20Q1 and onwards follows that of 19Q4. There will not be hg38 mutations until TCGA does the switch, and we are not aware of any plans for that.