Dear DepMap community,
Thank you for your sharing the public datasets for genetic information.
I have a simple question about the mutation information.
I would like to use maftools to visualize the somatic mutation data. I downloaded the file named “OmicsSomaticMutations.csv”. But the read.maf function could not read the data, because the column names of the data are different from the requirements of maftools package. Additionally, even though I could change the column names by myself, I still could not find the information about “End_position”.
Therefore, I would like to ask if there is any possibility of analyzing the data according to the workflow of TCGA in the next version so that we will be able to use the same r package to visualize these data.
Sorry for the delayed reply. Starting from 23Q2 we are releasing an additional mutation file called OmicsSomaticMutationsMAFProfile.maf which should be compatible with maftools. Please let us know if you run into any issues with this file!
Thank you very much. I noticed that and downloaded the OmicsSomaticMutationsMAFProfile to visualize several days ago.
But I still have a question. I also downloaded OmicsCNSegmentsProfile.csv and wanted to use it as input data for GISTIC2. I am not sure if it is correct. Because I know that CCLE has no paired normal cells when the cancer cells were detected using the SNP6.0 array, which is the difference compared with the data derived from TCGA.
Apologies but I’m not sure I understand your question - we did use to have a lot of SNP array copy number data but now they have been replaced by either WES or WGS, and you are correct that DepMap currently doesn’t have matched normal data. I personally am not familiar with GISTIC and not sure if the OmicsCNSegmentsProfile.csv file can be directly plugged in.