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Text: The WES samples ( FASTQ files ) were processed using sarek ( v2.7.1 ) 40 . Briefly , the following steps were performed : quality filtering and adaptor trimming with TrimGalore ; alignment to the reference genome with BWA ; marking of duplicates with GATK4 MarkDuplicates ; recalibration of scores with GATK4 BaseRecalibrator and ApplyBSQR ; and computing of pileups with SAMtools . Variant calling was performed using four different tools : Mutect2 , Strelka2 , MSIsensor and Control - FREEC ( tumor - only and pair mode ) . Filtering of the variants generated by Mutect2 was conducted using GATK4 GetPileupSummaries , CalculateContamination and FilterMutectCalls . Annotation of the variants was performed using snpEff . MultipleQC and statistics were generated using FastQC , Qualimap , SAMtools , VCFtools and MultiQC . We used a public Panel of Normals ( PON ) obtained from the public repository of GATK at gs://gatk - best - practices/ somatic - hg38/1000g_pon.hg38.vcf.gz and a BED file containing all the genomic intervals of the kits used to generate the WES samples . Mutect2 variants corresponding to the tumor - only samples were refiltered with GATK4 FilterMutectCalls using a value of 10 for the parameter ' -max - events - in - region ' . These variants were subsequently reannotated with snpEff with the same genome reference , version and settings that were used in the processing pipeline . The generated mutational data were subsequently summarized , postprocessed , filtered and validated for downstream analysis .<|eot_id|><|start_header_id|>assistant<|end_header_id|>

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