Figure 2

Directed acyclic graphs of GATK and Dindel workflows. Directed acyclic graphs to describe GATK (A) and Dindel (B) workflows are generated by Pwrake, manually adjusted, and visualized using Graphviz. (A) depicts a workflow from a *.bam file to an all_snvs.filtered.vcf, while (B) depicts a workflow from a *.bam file to a *.dindel.vcf file. Tasks to process the *.dindel.realign_windows.N.txt files are dynamically generated during the embarrassingly parallel stage (stage 3) depending on *.dindel.libraries.txt and *.libralies.txt. Prior to stage 3, an option "--numWindowsPerFile 1000" is applied to makeWindows.py to generate 11 files containing windows. File *.didndel_reagion_window is a dummy file representing all the *.dindel.realign_windows.N.txt files.