I am currently analyzing TCGA data in term of germline variant calling. And as expected, for some cases I got both blood and tissue sample for the normal. This information can easily be found in the corresponding TCGA barcode ( https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode ).
My idea is to use this to remove possible false positive, i.e. if a variant is not found in both samples (blood and tissue), I would to remove it.
Does anyone see a problem I didn't think about? Do you think it is a better idea to keep all blood variant (better quality than tissue), and add a variant from tissue if the QUAL is much higher?