= Updating to Reggie 4.13 = === Genotyping with !HaplotypeCaller in the Hisat pipeline === In `reggie-config.xml` the following changes are required (included in the default configuration that is shipped with Reggie): * In the `` section, a `` sub-section should be added with the full `` to a Java executable. It must be at least Java 8 since GATK will not work with earlier versions. * In the `` section, a `` sub-section should be added with the full `` to the Genome Analysis Toolkit JAR file (https://software.broadinstitute.org/gatk/download/). * In the `` section, three new configuration options need to be added: - ``: Path to FASTA file used to create the reference that Hisat is aligning against. - ``: Path to a VCF file with SNP definitions that we are looking for. - ``: Other static options for the !HaploypeCaller. Note that the paths are relative the `` directory.