Methods and scripts for "The role of germline TE insertions in pediatric cancer predisposition".

Software required

• xTea
• AEon
• goleft/indexcov
• bcftools, python (pyranges)

Scripts

• run_xtea.sh to generate xTea calls.
• postprocess_xTea/postprocess_xTEA.sh to annotate and merge xTea calls within 35bp
• sample_filtering_steps/run_nextflow_meiqc.sh to get ancestry, depth, and indexcov estimates
• For ancestry-matched control cohort generation see matched_control_generation/