2. STEP-BY-STEP MODE TUTORIAL
In step-by-step mode, the user can individually run each step for calling and annotation of SNP and Indels from DNA and RNAseq data as a workflow created basis best practice guidelines on SPMI analysis based on the GATK (McKenna, et al. 2010; DePristo, et al. 2011; Cibulskis, et al. 2013) and VarScan2 (Koboldt, et al. 2012), plus other tools including
the Variant Effect Predictor (VEP) of Ensembl (McLaren, et al. 2016) for variant annotation. In step-by-step mode, each step of the analysis (for instance, quality analysis, preprocessing, mapping, postprocessing, variant calling, etc.) to be completed separately and in different interfaces.
