Whole exome sequencing
Quality control of WES was performed on raw data using fastQC (v. 0.11.8) (Sequencing reads were aligned to the Human reference genome (UCSC genome assembly GRCh37/hg19) using Burrows-Wheeler AlignerSomatic single-nucleotide variants (SNVs) and indels calling were performed using Sentieon Genomic Tool v. 201911Putative false positive calls have been removed considering as filters: (i) the variant-supporting read count greater than 2; (ii) variant allele frequency greater than 0.05; (iii) average variant position in variant-supporting reads (relative to read length) >0.1 and lower than 0.9; (iv) average distance to effective 3′ end of variant position in variant-supporting reads (relative to read length) greater than 0.2; (v) fraction of variant-supporting reads from each strand >0.01; (vi) average mismatch quality difference (variant—reference) lower than 50; vii) average mapping quality difference (reference—variant) lower than 50. Annotation of SNVs and indels was performed using AnnoVar