New Gene-Level Tool Enhancements and Gene Expression API Now in the GDC 2.2 McClintock Release!
In the GDC 2.2 McClintock Release, the following features have been released:
Analyze Data
GDC Data Dictionary 3.1 Expands Diagnosis Information, TCGA Properties, and Bioinformatics Workflows
GDC Data Dictionary 3.1 expands diagnosis information, TCGA properties, and bioinformatics workflows:
New Cohort Level MAF Tool and Enhancements in GDC 2.0
Introducing the latest advancements in GDC 2.0 with Release 2.1! Here's what's new:
Introducing GDC 2.0: A New Cohort-Centric Design
The GDC has released GDC 2.0 which expands on the GDC Data Portal initially launched in 2016 by providing a cohort-centric design and new analysis tools. GDC 2.0 features include:
Why do some projects with WGS structural variant data have BEDPE files and some projects do not?
Submitted by Anonymous
on
Generally any WGS data should have associated structural variant files (BEDPE) except in the cases in which either there are no tumor/normal matches or when variant calling has not been implemented yet.
Why did the GDC remove SomaticSniper?
Submitted by Anonymous
on
The SomaticSniper whole exome variant caller was one of the first generation somatic mutation callers developed by the scientific community. It works the best with blood cancer that has high level of tumor-in-normal contaminations, but is often overly permissive for solid tumors. Since our first data release in 2016, the GDC has gradually adopted newer tools or new tool versions, and has transited the focus of somatic variant calling from any single caller to multi-caller ensemble.
Does the GDC provide access to germline variants?
Submitted by Anonymous
on
Any germline SNP calls are not available for exploration in the GDC Data Portal. Instead, alignments for germline data are available under controlled access. Users with appropriate access may use the alignments to generate germline variants.
Some somatic variants callers, such as MuTect2, also output somatic calls with some level of germline possibilities, such as those labelled as "germline_risk". Please note that these calls are, by no means, germline variants. They are somatic calls with boundary probability of germline risks.