My goal is to assign a mutation status to samples from LGG and GBM, but it's not clear to me which samples should be NA and which should be annotated as WT.
Tis topic was touched on in this thread: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
Basically, it seems to be the case that one can identify samples from which calls were made by subsetting to samples that meet coverage thresholds via this data: https://www.synapse.org/#!Synapse:syn1695394, and thus identify samples that were excluded from being called vs. samples in which no variant was detected.
This link points to coverage for data aligned to hg19. Does the same data exist somewhere for hg38?