Fig. 1
From: Germline contamination and leakage in whole genome somatic single nucleotide variant detection
GermlineFilter Workflow for the SMC Challenge. Locally, tumour-normal BAM files are submitted to a germline caller (e.g. GATK) to create a germline SNP call VCF file, which is later hashed and encrypted. The encrypted, hashed germline calls can now be moved to any server and used to filter for germline leakage in somatic SNV call VCF files. The output is the germline count found in the somatic calls. To quantify germline leakage using the Challenge submissions, the germline variant VCF file was created by the Challenge administrators “in-house” on a private server. The somatic SNV prediction VCF files were provided by the teams participating in the Challenge