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.