Dear DepMap team,
Currently, we are using the DepMap somatic mutations data in one of the our projects, and find for the same ModelID, there are more mutation calls in the OmicsSomaticMutations.csv file of the 23Q2 release. For example, for ACH-000336, there are 32 more mutation calls in 23Q2 release compared to 22Q4 release, please see attached files for more details.
Is there any differences between the 23Q2 and 22Q4 mutation caller pipeline? would you help/explain?
Thanks very much,
ACH-000336_OmicsSomaticMutations_22Q4.csv (84.3 KB)
ACH-000336_OmicsSomaticMutations_23Q2.csv (114.4 KB)
Thanks for your feedback!
We have been working on updating our mutation annotation and filtering pipeline, and at some point between 22Q4 and 23Q2 we ran a test of a slightly different logic on this particular sample that got included in the official release accidentally, which is why there were more mutations in 23Q2 for this sample specifically. There is no change in the mutation pipeline between the two releases and this accident shouldn’t affect other samples.
As a heads up, we are hoping to roll out our updated mutation pipeline in the upcoming release, so the mutation calls are going to be different (and better!). Sorry about the confusion.