
## HG002

Rscript plot_ROC.R Figure_6 \
  roc_data_files_v1.5/HG002/BWA-MEM:"BWA-MEM" \
  roc_data_files_v1.5/HG002/Giraffe-HPRC:"Giraffe(HPRC_pangenome)" \
  roc_data_files_v1.5/HG002/Giraffe-diploid:"Giraffe(diploid)" \
  roc_data_files_v1.5/HG002/Giraffe-imputefirst-c20:"Giraffe(Imputefirst_c20)" \
  roc_data_files_v1.5/HG002/LevioSAM2-imputefirst-c20:"LevioSAM2(Imputefirst_c20)" \
  roc_data_files_v1.5/HG002/Giraffe-benchmark:"Giraffe(benchmark)" \
  roc_data_files_v1.5/HG002/LevioSAM2-benchmark:"LevioSAM2(benchmark)"

## grouped plot for HG001 HG003 HG004 HG005 samples - to show in supplementary

Rscript rocplot-grouped.R Figure_S9 \
  "HG001:roc_data_files_v1.5/HG001/BWA-MEM:BWA-MEM,roc_data_files_v1.5/HG001/Giraffe-HPRC:Giraffe(HPRC_pangenome),roc_data_files_v1.5/HG001/Giraffe-diploid:Giraffe(diploid),roc_data_files_v1.5/HG001/Giraffe-imputefirst-c20:Giraffe(Imputefirst_c20),roc_data_files_v1.5/HG001/LevioSAM2-imputefirst-c20:LevioSAM2(Imputefirst_c20),roc_data_files_v1.5/HG001/Giraffe-benchmark:Giraffe(benchmark),roc_data_files_v1.5/HG001/LevioSAM2-benchmark:LevioSAM2(benchmark)" \
  "HG003:roc_data_files_v1.5/HG003/BWA-MEM:BWA-MEM,roc_data_files_v1.5/HG003/Giraffe-HPRC:Giraffe(HPRC_pangenome),roc_data_files_v1.5/HG003/Giraffe-diploid:Giraffe(diploid),roc_data_files_v1.5/HG003/Giraffe-imputefirst-c20:Giraffe(Imputefirst_c20),roc_data_files_v1.5/HG003/LevioSAM2-imputefirst-c20:LevioSAM2(Imputefirst_c20),roc_data_files_v1.5/HG003/Giraffe-benchmark:Giraffe(benchmark),roc_data_files_v1.5/HG003/LevioSAM2-benchmark:LevioSAM2(benchmark)" \
  "HG004:roc_data_files_v1.5/HG004/BWA-MEM:BWA-MEM,roc_data_files_v1.5/HG004/Giraffe-HPRC:Giraffe(HPRC_pangenome),roc_data_files_v1.5/HG004/Giraffe-diploid:Giraffe(diploid),roc_data_files_v1.5/HG004/Giraffe-imputefirst-c20:Giraffe(Imputefirst_c20),roc_data_files_v1.5/HG004/LevioSAM2-imputefirst-c20:LevioSAM2(Imputefirst_c20),roc_data_files_v1.5/HG004/Giraffe-benchmark:Giraffe(benchmark),roc_data_files_v1.5/HG004/LevioSAM2-benchmark:LevioSAM2(benchmark)" \
  "HG005:roc_data_files_v1.5/HG005/BWA-MEM:BWA-MEM,roc_data_files_v1.5/HG005/Giraffe-HPRC:Giraffe(HPRC_pangenome),roc_data_files_v1.5/HG005/Giraffe-diploid:Giraffe(diploid),roc_data_files_v1.5/HG005/Giraffe-imputefirst-c20:Giraffe(Imputefirst_c20),roc_data_files_v1.5/HG005/LevioSAM2-imputefirst-c20:LevioSAM2(Imputefirst_c20),roc_data_files_v1.5/HG005/Giraffe-benchmark:Giraffe(benchmark),roc_data_files_v1.5/HG005/LevioSAM2-benchmark:LevioSAM2(benchmark)"
