Data analysis
tumor
TUMOR
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic version 0.38. The trimmed reads were mapped to the reference genome using the Illumina DRAGEN Bio-IT Platform. BAM files were generated as a result of this step. Somatic variants were called using the Illumina DRAGEN Bio-IT Platform in somatic mode. Paired normal samples were used in the process, if provided, or a panel of normal was used to remove technical artifacts. Variants were further filtered and any variants in the following categories were considered false positives and removed: (1) marked as common variants in dbSNP build 151; and (2) non_cancer_AC > 5 in the gnomAD exome database r2.1.1. The filtered VCF was then annotated with Ensembl Variant Effect Predictor version 95. For each variant that was mapped to the reference genome, all overlapping Ensembl transcripts were identified and the effects that each allele of the variant may have on each transcript were predicted by Variant Effect Predictor. The set of consequence terms was defined by the Sequence Ontology. The most severe impact was selected for each variant and they were used for downstream cohort analysis. The impacts of the variants were classified based on MAF document specifications. The tumor mutation load was calculated based on the number of mutations in the genome region that was targeted.