jhu-indexes-dataset/s3://genome-idx/impute-first/scripts-v1

##Impute-First Data Files 

#Benchmarking_Files/
	* HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz - GIAB HG001 Benchmark VCF
	* HG001_GRCh38_1_22_v4.2.1_benchmark.bed - GIAB HG001 Benchmark BED (High-conifdence regions)
	* GRCh38_mrg_full_gene.bed - GIAB GRCh38 CMRG regions
	* GRCh38_stratifications/extract_common_HG001_benchmark_sites.sh - Script identifying common regions in HG001 benchmarking and GRCh38 stratifications. Bed files with a 'confident_' prefix are outputs of the script.
	* GRCh38_stratifications/BED files: 
		* [GRCh38_MHC.bed, 
		   GRCh38_allOtherDifficultregions.bed, 
                   GRCh38_alldifficultregions.bed, 
                   GRCh38_alllowmapandsegdupregions.bed] 
		* [confident_GRCh38_MHC.bed, 
		   confident_GRCh38_allOtherDifficultregions.bed,
                   confident_GRCh38_alldifficultregions.bed, 
                   confident_GRCh38_alllowmapandsegdupregions.bed]

#Personalized_HG001_calls/ - Impute-first(IF) generated personalized variant callsets for HG001. 
	* [IF_bbbc5.vcf.gz,
	   IF_bbgc5.vcf.gz,
	   IF_rgc1.vcf.gz,
	   IF_rgc5.vcf.gz]

#Workflow_GATK-HC_outputs/ - Downstream Variant Calling outputs generated using GATK-HC on Workflows discussed in Impute-first framework. 
	* [BWAMEM_HG001.vcf.gz, 
	  bbbc5_HG001.vcf.gz, 
	  bbgc5_HG001.vcf.gz, 
	  pangenome_HG001.vcf.gz, 
	  rgc1_HG001.vcf.gz, 
	  rgc5_HG001.vcf.gz,
	  vglinear_HG001.vcf.gz]

#Supplementary_Tables/ 
	* Table_S1.csv: Alignment score comparison between the rgc1-imputed diploid personalized reference and the standard linear GRCh38 reference.
	* Table_S2.csv: Variant calling performance metrics for HG001 real donor reads, stratified by SNVs, indels, and overall variants, across different reference combinations within GIAB HG001 high-confidence regions.
	* Table_S3.csv: Variant calling performance metrics for HG001 real donor reads for overall variants, across different reference combinations within GIAB GRCh38 Complex Medically Relevant Gene (CMRG) regions.
	* Table_S4.csv: Variant calling performance metrics for HG001 real donor reads for overall variants, across different reference combinations within GIAB GRCh38 stratifications.
	* Table_S5.csv: Time and memory taken by each VG Giraffe-based workflow in the personalization, downstream indexing, and downstream alignment steps.
	* Table_S6.csv: Index and graph size measurements for the VG Giraffe graphs generated in various workflows.