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VaDiR workflow for processing somatic variant calls from RNA-seq. Sequence alignment is done by STAR and BWA MEM for RNA and DNA, respectively. The refined mapping follows GATK Best Practices. The variant calling is done by Unified Genotyper (GATK) and MuTect2 (GATK). The following filtering steps are done by RVBoost and SNPiR. Additional filters such as MAQ > 40, germline read depth (DP) > 5, and germline variant fraction (VAF) < 0.03 are applied to remove germline variants.
