PythonSTRing

This repository was used for a study towards the use of STR calling tools with whole exome sequencing data in a diagnostic environment. This study was commissioned by the genetic diagnostics department at the UMC Utrecht.

The bash script "sbatch_Pypeline.sh" was used to commit Python pipelines to the Slurm workload manager for automatic analyses of sample BAM files in a given directory.

For the tools ExpansionHunter and LobSTR separate bash scripts have been made that were customised for these tools and include implementation of an Rscript to plot and visualise results.

These bash scripts must be given the Python pipeline and full paths to the input and output directories as arguments.

Python pipelines for ExpansionHunter LobSTR and STRetch can be found in this repository, along with conversion scripts for output files into a CSV file for ExpansionHunter and LobSTR.

The Python script "Processing_LobSTR.py" was used in the study to filter results for genes AR, ATXN3, C9ORF72 and DMPK as these were the genes that were included in the study.