I am looking for already called and annotated germline and somatic snvs from different TCGA projects and have already been approved through dbGaP for the data access.
Unfortunately, it seems that in the harmonized data portal during variant calling all germline mutations are already filtered out (even in controlled access files) - please correct me, if I am wrong.
Therefore, as recommended in this post: How do I obtain germline mutation for TCGA samples? , I am planning to switch to the legacy data.
Here, it seems that most patients have been analyzed via two platforms, Illumina Hiseq and Illumina GA. Do you know which of those data is of higher quality and why both platforms have been used? Moreover, has anyone found some good documentation on how data of the legacy archive has been processed? (e.g. variant caller, ...).
Any help would be much appreciated!