Fig. 3.

Variant calling workflows under refinement in the development branch of docker4seq. a SNVs calling in DNA workflow. The function snvPreprocessing requires that users provides its own copy of the GATK software, because of Broad Institute license restrictions. This function returns a bam file sorted, with duplicates marked after GATK indel realignment and quality recalibration. b Data preprocessing for samples derived by Patient Derived Xenografths (PDX). The xenome function discriminates between the mouse host reads and the human tumor reads, then DNA or RNA SNV calling workflows can be applied. c SNVs calling in RNA workflow. The function star2steps generates a sorted bam, where duplicates are marked and processed by opossum for removal of intronic regions and merging of overlapping reads. The names followed by parenthesis are the docker4seq functions used to execute the analysis steps. Black indicate elements in common between more than one workflow