itd === The `itd` module is responsible for finding Internal Tandem Duplications in select genes, specifically *FLT3* and *KMT2A*. Tools ----- First, this module uses `bwa `_ to align the trimmed reads to a custom reference, which contains the transcript sequence of *FLT3* and *KMT2A*. Next, a custom tool, `rose-dt `_, is used to detect and visualise Internal Tandem Duplications, using evindence from soft-clipped reads. Input ----- The input for this module is a single pair of FastQ files per sample, specified in a PEP configuration file, as is shown below. .. csv-table:: Example input for the itd module :delim: , :file: ../../test/pep/itd.csv Output ------ The output of this module are a JSON file with an overview of the most important results, as well as a number of other output files: * For both *FLT3 and *KMT2A*, a .csv file with the detected tandem duplications. * For both *FLT3* and *KMT2A*, a figure to visualise the detected tandem duplications. Configuration ------------- The configuration for this module is tailored to the provided reference files, be very careful if you want to modify any of these settings. You can automatically generate a configuration for the fusion module using the `utilities/create-config.py` script. .. literalinclude:: ../../test/data/config/itd.json :language: json Configuration options ^^^^^^^^^^^^^^^^^^^^^ .. list-table:: Configuration options * - Option - Description - Required * - fasta - The fasta file containing the trasncript sequence for FLT3 and KMT2A - yes * - flt3_name - The name of the FLT3 sequence in the fasta file - yes * - flt3_start - The start of the FLT3 region to investigate - yes * - flt3_end - The end of the FLT3 region to investigate - yes * - kmt2a_name - The name of the KMT2A sequence - yes * - kmt2a_start - The start of the KMT2A region to investigate - yes * - kmt2a_end - The end of the KMT2A region to investigate - yes