The Realigner_Target_Creator handler uses the Genome Analysis Toolkit (GATK) v3.8 or earlier to create .intervals files to be used with Indel_Realigner. Important note: GATK 4 no longer has indel realignment functionality, please use GATK v3.8 or earlier for this step.

To run Realigner_Target_Creator, all common variables and handler-specific variables must be defined within the configuration file. Once the variables have been defined, Realigner_Target_Creator can be submitted to a job scheduler with the following command (assuming that you are in the directory containing sequence_handling):

./sequence_handling Realigner_Target_Creator Config_Indel_Realign

Where Config is the full file path to the configuration file.

The following are a list of variables that need to be defined within Config_Indel_Realign. In addition to the handler-specific variables, all common variables must be defined.

Realigner_Target_Creator generates a single .intervals file for each sample. The .intervals files can be found at

${OUT_DIR}/Realigner_Target_Creator

No changes are made to the input BAM files for this handler.

Realigner_Targets_Creator depends on the GATK v3.8 or earlier and Java. In addition, PBS is required for basic operation. Please check the dependencies page to ensure that you are using the required version of each dependency.