How is validation performed on genomic data (BAM files) submitted to the GDC?

Submitted BAM files are validated at the GDC for file integrity and format using md5sum checks, automated QC checks, and the Picard ValidateSamFiles tool. Sequencing quality is assessed using FASTQC, and additional quality metrics are gathered using tools like Picard and Samtools. Severe issues, such as high cross-sample contamination, may prevent the data from being released, but minor issues typically do not result in rejection. Instead, the GDC exposes many of the quality metrics so users may review them and do further filtering. For more details, please visit: GDC Data Harmonization.