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Fig. 2 | Genome Medicine

Fig. 2

From: Technological considerations for genome-guided diagnosis and management of cancer

Fig. 2

Example of a best practices SNV calling workflow for somatic exome and genome data (reproduced with permission from [80]). Raw reads from the sequencing instrument are aligned and duplicate reads are marked (using the Picard tool). Vendor-assigned base quality scores are recalibrated for accuracy (based on position in read and other factors). Before running somatic analysis, both tumor and normal read groups are assessed for contamination, such as sample swap, cross-contamination, and tumor contamination in the normal sample. Somatic variants are those passing filter variants that are present in the tumor but not in the matched-normal sample. Several filters are used to control for technical noise in the system, which includes the variant allele frequency and a panel of normals (for more details see Cibulskis et al. [45])

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