hello. first I am new to using depmap.
In depmap portal File Downloads there is only somaticmutation files such as OmicsSomaticMutations.maf, csv etc.
In the 22Q4 Mutation Pipeline Update i found some germline mutation will be resued define as important(tumor suppressors & oncogenes in OncoKB)
Then where can i find resued germline mutation? is it in the OmicsSomaticMutations files provided in depmap portal? or i have to download germline mutation file through terra(dont know how to use)?
lastly Im interested in ovarian cancer BRCA1,2 germline mutation.
Rescued germline mutations should be in the same file (OmicsSomaticMutations). However, our current filtering and rescue logic is flawed and we are working on updating it for the coming releases. If you find certain mutations missing, I’d recommend checking back after the next data release.
Sample-level mutation calls (including germline) can also be found in our public Terra workspace. Once you’re logged in, you can navigate to Data → sample, and the google cloud locations for mutation calls can be found under mutect2_vcf_wes and/or mutect2_vcf_wgs.
Hope this helps,