Part I: SV preprocessing
sv_preprocessing.sh

Part II: SV benchmarking
Figure_3A_data.txt
Figure_3A.Rmd

Part III: SV metrics
Figure_3B_3C_S7_S8_data.txt (On AWS at https://s3.amazonaws.com/1000g-ont/index.html?prefix=Gustafson_etal_2024_preprint_SUPPLEMENTAL/Figure_3B_3C_S7_S8_data.txt)
Figure_3B.Rmd 
Figure_3C.Rmd
Figure_S7.Rmd
Figure_S8.Rmd


Part IV: Cumulative unique SVs
unique_svs.sh
Figure_3D_data.txt
Figure_3D.Rmd

Part V: SV agreement between callers and confident callset 
sv_caller_agreement.sh
Figure_3E_S9_data.txt (On AWS at https://s3.amazonaws.com/1000g-ont/index.html?prefix=Gustafson_etal_2024_preprint_SUPPLEMENTAL/Figure_3E_S9_data.txt)
Figure_3F_data.txt
Figure_3E.Rmd
Figure_3F.Rmd
Figure_S9.Rmd

Part VI: SVs in medically relevant regions
sv_annotation.sh
OMIM_exons_hg38_sorted.bed
Figure_S12_data.txt
Figure_S12.Rmd
