Tools and dependencies AlleleCount 2.2.0 BWA 0.7.8 FastQC 0.11.5 freebayes GATK 3.7 gcc 4.9.2 java jdk 8 (we do need jdk7 for MuTect1) Manta 1.0.3 MultiQC 0.9 MuTect1 1.5 nextflow >= 0.22.1 perl 5.18.4 Picard 2.0.1 R 3.2.3 SAMTools 1.3 snpEff 4.2 Strelka 1.0.15