Somatic mutation data (hg38 reference genome)

Annotated .maf somatic mutation data files for 30 tumour samples from 22 patients <br> <strong>Method for somatic mutation calling</strong> Somatic single nucleotide variants (SNVs), insertions and deletions (InDels) were called using Mutect2 (v.4.1.8) and Strelka (v. 2.9.10) respectively from matched normal and tumour pairs. Strelka was run with the --exome option (for WXS data only) and –callRegions option to restrict mutation calling to chr1-22,X,Y,M. In order to filter for false positive somatic mutation calls such as common variants and mapping artifacts, Mutect2 was run with gnomAD germline population reference and a panel of normal (PON) samples, generated using the CreateSomaticPanelOfNormals function part of the GATK4 (v.4.1.8) best practise pipeline. FFPE samples are known to contain mutational biases in the C&gt;T/G&gt;A transition. OxoG filter was applied through the read orientation bias model with Mutect2 to remove mutations with FFPE strand bias. GATK4 GetPileupSummaries and CalculateContamination was used with a set number of known germline common variants reported in ExAC at a population minor allele frequency &gt; 0.05 to calculate cross sample contamination. FilterMutectCalls was run using default parameters. Filtered Mutect2 and Strelka somatic variant calls were combined into one vcf using GATK3 (v.3.8.1) CombineVariants. Bcftools (v.1.12) (http://samtools.github.io/bcftools/bcftools.html) <em>norm</em> function was used to left align and normalise InDels. Variants passing quality control were annotated using MSK vcf2maf (https://github.com/mskcc/vcf2maf) and variant effect predictor (VEP v.96) using GRCh38, which outputs both a .vcf and .maf file format. Annotated maf files were used for downstream somatic mutation analysis.