Closed fpbarthel closed 5 years ago
@moskalika @Kcjohnson please comment on completeness of sex information for new dataset as well as any (pending) updates to the old data
@fpbarthel we have all genders except for 2 Dana-Farber cases; we are waiting for clinical data from them.
I also made a few changes to the clinical.surgeries table (consolidating one patient; adding TMZ info for 7 surgeries which are now '0'; initial diagnosis histo/grade/surg_interval)
We do not currently have any patient sex information from the DKFZ cohort. We may receive this information at a later point, but there's no guarantee. If chrX and chrY were not removed from the sequencing data, we may be able to reliably infer this information.
@moskalika just to confirm that:
GLSS-DF-0013
GLSS-DF-0014
GLSS-MD-0085
GLSS-MD-0119
GLSS-MD-0120
GLSS-MD-0126
GLSS-MD-0135
GLSS-MD-0138
GLSS-MD-0140
GLSS-MD-0141
@fpbarthel we are waiting for clinical data for the two DF cases. The MD Anderson cases from the first data freeze will not have genders.
CNV data is now complete, closing issue
To-do list of items related to finalizing CNV callset for data release 2.
Aneuploidy value
metric to scan for 0.0 samples that indicate no CNVs. These should be re-evaluated for blocklist.