Clonality
tumour
FRAMESHIFT MUTATION, TUMOUR
Whole-exome sequence reads of tumour–normal paired samples of patients were aligned to the reference human genome (hg19) using the Burrows–Wheeler alignment tool (bwa mem v.0.7.17) and samtools (v.1.6). Duplicates were marked with picard-2.11.0 MarkDuplicates (MuTect 1.1.7 and Strelka 1.0.15 were used to call SNV and indels on pre-processed sequencing data. For the MuTect calls, dbSNP 138 and CosmicCodingMuts.vcf (v.86)To infer clonality of vaccine targets, we extracted missense and frameshift mutations from the filtered VCF files, and these mutations were put into the PhyloWGS software package (