Whole-exome sequencing data analysis
Cancer
MUTANT, CANCER
Reads in the FASTQ format were aligned to the reference human genome GRCh37 using the Burrows–Wheeler aligner (BWA version 0.7.17). Local realignment was performed using the Genome Analysis Toolkit (GATK version 4.13.0). Duplicate reads were removed using Picard version 2.5. In case of matched tumor-normal samples, somatic single-nucleotide variants (SNVs) were identified using a validated pipeline that integrated mutation calls from three different mutation callers. SNVs were called with VarScan (version 2.4.3)TMB was calculated using the number of significant SNVs (with untranslated transcribed regions, synonyms, introns and intergenic SNVs filtered out) divided by the number of megabases covered at a defined level. To identify tumor-specific mutant peptides, pVAC-Seq (personalized Variant Antigens by Cancer Sequencing) was used (pVACtools version 1.5.4)