Somatic variants calling
tumor
TUMOR
WES data were aligned to the hg38 reference genome using BWA (v.0.7.12). Duplicate reads were then removed by Picard (v.1.84). Local realignment and base quality score recalibration were carried out using GATK (v.4.1). Single nucleotide variants, small insertions and deletions were detected using SomaticSniper (v.1.0.5.1), MutTect2 (v.2.7.0), MuSE (v.1.0), Strelka (v.2.9.9) and Svaba (v.0.2.1), then annotated by ANNOVAR (v.180504). Single nucleotide variants were filtered to identify nonsynonymous exonic variants. Mutational signatures were determined using deconstructSigs (v.1.8.0) with default parameters applying COSMIC v.2 signatures as the reference with a maximum of two signatures. Copy number variants, tumor purity and ploidy were called using FACETS (v.0.16.0). Significantly amplified or deleted regions of copy number variants were identified by GISTIC (v.2.0.23).