2.5. Variant Calling and Filtering for Analysis of the bTMB and Other Candidate Biomarkers
Mutect
Somatic variant calling of single-nucleotide variants (SNVs) and short insertions and deletions (InDels) for each ctDNA were conducted with the matched buffy coat DNA, using Mutect (version 1.1.6) and the SomaticIndelocator tool in the GATK. Common variants from the somatic variant candidates were filtered out with the common dbSNP (build 141; found in >1% of samples), Exome Aggregation Consortium (ExAC; r0.3.1, threshold frequency 0.001), Korean Reference Genome database (KRGDB) and an in-house panel of normal variants. Final somatic variants were annotated using the Variant Effect Predictor (version 79, accessed on 1 September 2021) and then converted to a maf file using vcf2maf (