7 research outputs found
Additional file 4: Table S2. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
Filtering Metrics. The criteria used to initially classify a variant in the training set for the quadratic discriminant model. (DOCX 14Â kb
Additional file 6: Figure S3. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
Mapping coverage as a function of variant calls. (PNG 38Â kb
Additional file 5: Table S3. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
One thousand Genomes Population Codes. Abbreviations used to describe the populations from the 1000 Genomes Project. (DOCX 17Â kb
Additional file 3: Figure S1. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
Somatic Variant Calling Workflow. Illustrates a detailed workflow of the somatic variant calling process. The steps from âTranspose to pileupâ and below are performed by the lumosVar software. (PNG 151Â kb
Additional file 2: Table S1. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
Definition of True Variants. Describes the criteria for counting a variant as a true variant. Germline variants were called by haplotype caller, samtools, and freebayes. Somatic variants were called by Mutect, Seurat, and Strelka. (DOCX 15Â kb
Additional file 9: Figure S5. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
Copy Number and Sample Fraction Across Dilutions. The copy number (left), minor allele copy number (center) and sample fraction of the copy number events (right) are plotted as heatmaps. (PNG 35Â kb
Additional file 8: Figure S4. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling
Variant Quality Filtering Across Dilutions. Shows the number of variants of each type, in each quality filtering category. Each graph represents a variant type, each bar represents a dilution, and the color of the bar represents the number of variants in each quality category. High quality positions have a PT > 0.99. Low quality positions have a PT < 0.99 but PV > 0.99. Artifacts have a PV < 0.99 and non variants are not considered by the tumor only caller (NaN). (PNG 43 kb