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How can I find high coverage whole genome sequencing (WGS) data?

Submitted by gaheens on

The GDC categorizes whole genome sequencing (WGS) coverage using the wgs_coverage property, which groups BAM files into four range buckets: 0x-10x, 10x-25x, 25x-150x, and 150x+. "High coverage" WGS in the GDC generally refers to alignments with a mean depth of 25x or greater — meaning, on average, each base in the genome is covered by at least 25 sequencing reads. This threshold reflects the minimum depth at which variant calling pipelines (SNV, indel, and structural variant) achieve reliable sensitivity and specificity for somatic mutation detection in cancer genomics.

Can GDC data be used in commercial and academic tools?

Submitted by gaheens on

GDC data available as open-access data can be used with proper accreditation. Use of controlled-access data requires dbGaP access and users must abide by the data use agreement (DUA) associated with the study. See GDC Data Access and Sharing Policies or contact the NCI Office of Data Sharing directly for further clarification: NCIOfficeofDataSharing@mail.nih.gov.

Why does TCGABiolinks no longer work when retrieving diagnosis?

Submitted by gaheens on

TCGA clinical data was expanded in GDC Data Releases 42 and 43. TCGA clinical data used to have one diagnosis per case. With the clinical data expansion, it is possible that a TCGA case has multiple diagnoses. This could be due to pre-enrollment diagnoses or other reasons. To properly query for the diagnosis information associated with the molecular data, the primary disease flag should be set to true (i.e., diagnosis_is_primary_disease = true).

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