= Updating to Reggie 4.13 =

=== Genotyping with HaplotypeCaller in the Hisat pipeline ===

In `reggie-config.xml` the following changes are required:

 * In the `<programs>` section, a `<java>` sub-section should be added with the full `<path>` to a Java executable. It must be at least Java 8 since GATK will not work with earlier versions.

 * In the `<programs>` section, a `<gatk>` sub-section should be added with the full `<path>` to the Genome Analysis Toolkit JAR file (https://software.broadinstitute.org/gatk/download/). 

 * In the `<align-hisat>` section, three new configuration options need to be added:

  - `<haplotypecaller-ref>`: Path to FASTA file used to create the reference that Hisat is aligning against
  - `<haplotypecaller-dbsnp>`: Path to a VCF file with SNP definitions that we are looking for
  - `<haplotypecaller-options>`: Other static options for the !HaploypeCaller

Note that all paths are relative the `<reference-dir>` directory.