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mschubert / TCGAbiolinks-downloader

GNU Make-driven workflow to download TCGA data via the TCGAbiolinks package
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Check known somatic variants that can also be germline #4

Open mschubert opened 6 years ago

mschubert commented 6 years ago

e.g. there was an issue with some oncogenic TP53 variants being filtered because they also occurred in germline

mschubert commented 6 years ago

This might be solved:

GERMLINE VARIANTS At this time, germline variants are deliberately excluded as harmonized data. The GDC does not recommend using germline variants that were previously detected and stored in the Legacy Archive as they do not meet the GDC criteria for high-quality data.

BRCA data (release 10), there is 5 patients with rs121912651 and 342 total with TP53 mutations (out of 986 samples)

This might be all of the ones that were filtered out in release 5?