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Used for issue tracking of data curation efforts.
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Alllele counts in TCGA PAAD MAF #103

Open n1zea144 opened 8 years ago

n1zea144 commented 8 years ago

TCGA pancreatic cancer study is missing allele counts. Can you please look into why this might be? The MAFs I find in Firehose seem to have them, at least this one:

http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/PAAD/20160128/gdac.broadinstitute.org_PAAD.Mutation_Packager_Oncotated_Raw_Calls.Level_3.2016012800.0.0.tar.gz.

We don’t use the Oncotated file, we use the following file (but I did a quick spot check and see allele counts there):

gdac.broadinstitute.org_PRAD.Mutation_Packager_Calls.Level_3.2015082100.0.0.tar.gz

We need to look into this further. My guess is its might be a MAF2MAF issue which a switch to analysis wouldn’t address.

zheins commented 8 years ago

Allele counts are missing in the mutations data for 8/21/2015. Data for 1/2016 (which Niki referenced) does have this data. The latest analyses data is 8/21/2015, so no good way to fix this issue without having mutations and analyses data out of sync.