Benchmarking Resources

Our Benchmarking Sample Manifest includes predefined input files (such as CRAM/BAM and VCF) along with corresponding expected outputs in JSON format, generated by the reference QC tool.

We execute our benchmarking pipelines on publicly available WGS data specifically, Genome in a Bottle (GIAB) samples from the 1000 Genomes Phase 3 Reanalysis, accessible through the Registry of Open Data on AWS.

The 1000 Genomes dataset generated by Illumina DRAGEN Germline is widely adopted across the genomics community, including in major population-scale efforts such as the UK Biobank and the All of Us Research Program. To promote diversity and representation, we curated a subset of 100 samples from this dataset, ensuring balanced coverage across multiple populations and both genders.

Sample_name	Sex	Biosample_ID	Population_code	Population_name	Superpopulation_code	Superpopulation_name	Population_elastic_ID	Data_collections
HG00100	female	SAME125154	GBR	British	EUR	European Ancestry	GBR	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00101	male	SAME125153	GBR	British	EUR	European Ancestry	GBR	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00102	female	SAME123945	GBR	British	EUR	European Ancestry	GBR	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00103	male	SAME125151	GBR	British	EUR	European Ancestry	GBR	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00176	female	SAME124956	FIN	Finnish	EUR	European Ancestry	FIN	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00177	female	SAME124957	FIN	Finnish	EUR	European Ancestry	FIN	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00183	male	SAME123642	FIN	Finnish	EUR	European Ancestry	FIN	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00185	male	SAME123648	FIN	Finnish	EUR	European Ancestry	FIN	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
HG00403	male	SAME123160	CHS	Southern Han Chinese	EAS	East Asian Ancestry	CHS	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
HG00404	female	SAME123158	CHS	Southern Han Chinese	EAS	East Asian Ancestry	CHS	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
HG00551	female	SAME124252	PUR	Puerto Rican	AMR	American Ancestry	PUR	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
HG00552	male	SAME124253	PUR	Puerto Rican	AMR	American Ancestry	PUR	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG00759	female	SAME125020	CDX	Dai Chinese	EAS	East Asian Ancestry	CDX	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG00766	female	SAME124458	CDX	Dai Chinese	EAS	East Asian Ancestry	CDX	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG00844	male	SAME123952	CDX	Dai Chinese	EAS	East Asian Ancestry	CDX	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01028	male	SAME123524	CDX	Dai Chinese	EAS	East Asian Ancestry	CDX	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01112	male	SAME123485	CLM	Colombian	AMR	American Ancestry	CLM	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
HG01113	female	SAME123484	CLM	Colombian	AMR	American Ancestry	CLM	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
HG01114	female	SAME123483	CLM	Colombian	AMR	American Ancestry	CLM	1000 Genomes 30x on GRCh38,Human Genome Structural Variation Consortium, Phase 2,1000 Genomes phase 3 release
HG01121	male	SAME1840127	CLM	Colombian	AMR	American Ancestry	CLM	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01500	male	SAME124941	IBS	Iberian	EUR	European Ancestry	IBS	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01501	female	SAME124942	IBS	Iberian	EUR	European Ancestry	IBS	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01502	male	SAME124943	IBS	Iberian	EUR	European Ancestry	IBS	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01507	female	SAME124948	IBS	Iberian	EUR	European Ancestry	IBS	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01565	male	SAME124566	PEL	Peruvian	AMR	American Ancestry	PEL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01566	female	SAME124564	PEL	Peruvian	AMR	American Ancestry	PEL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01567	female	SAME124565	PEL	Peruvian	AMR	American Ancestry	PEL	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01571	male	SAME124346	PEL	Peruvian	AMR	American Ancestry	PEL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01583	male	SAME1839895	PJL	Punjabi	SAS	South Asian Ancestry	PJL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01595	female	SAME123569	KHV	Kinh Vietnamese	EAS	East Asian Ancestry	KHV	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01596	male	SAME125227	KHV	Kinh Vietnamese	EAS	East Asian Ancestry	KHV	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,Human Genome Structural Variation Consortium, Phase 2,1000 Genomes phase 3 release
HG01597	female	SAME125226	KHV	Kinh Vietnamese	EAS	East Asian Ancestry	KHV	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01840	male	SAME123552	KHV	Kinh Vietnamese	EAS	East Asian Ancestry	KHV	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01879	male	SAME1839037	ACB	African Caribbean	AFR	African Ancestry	ACB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01880	female	SAME1839109	ACB	African Caribbean	AFR	African Ancestry	ACB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01881	female	SAME1839193	ACB	African Caribbean	AFR	African Ancestry	ACB	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG01882	male	SAME122849	ACB	African Caribbean	AFR	African Ancestry	ACB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG02461	male	SAME1839993	GWD	Gambian Mandinka	AFR	African Ancestry	GWD	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,Gambian Genome Variation Project (GRCh38)
HG02462	female	SAME1839991	GWD	Gambian Mandinka	AFR	African Ancestry	GWD	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,Gambian Genome Variation Project (GRCh38)
HG02463	male	SAME1839983	GWD	Gambian Mandinka	AFR	African Ancestry	GWD	1000 Genomes 30x on GRCh38
HG02465	female	SAME1839973	GWD	Gambian Mandinka	AFR	African Ancestry	GWD	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,Gambian Genome Variation Project (GRCh38)
HG02490	male	SAME1839625	PJL	Punjabi	SAS	South Asian Ancestry	PJL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG02601	female	SAME1840293	PJL	Punjabi	SAS	South Asian Ancestry	PJL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG02922	female	SAME1839441	ESN	Esan	AFR	African Ancestry	ESN	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG02923	male	SAME1839436	ESN	Esan	AFR	African Ancestry	ESN	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG02924	male	SAME1839516	ESN	Esan	AFR	African Ancestry	ESN	1000 Genomes 30x on GRCh38
HG02945	female	SAME1839075	ESN	Esan	AFR	African Ancestry	ESN	1000 Genomes 30x on GRCh38
HG03052	female	SAME1839496	MSL	Mende	AFR	African Ancestry	MSL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03054	male	SAME1839507	MSL	Mende	AFR	African Ancestry	MSL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03056	male	SAME1839518	MSL	Mende	AFR	African Ancestry	MSL	1000 Genomes 30x on GRCh38
HG03073	female	SAME1839019	MSL	Mende	AFR	African Ancestry	MSL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03593	male	SAME1839171	BEB	Bengali	SAS	South Asian Ancestry	BEB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03598	female	SAME1839194	BEB	Bengali	SAS	South Asian Ancestry	BEB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03604	female	SAME1840236	BEB	Bengali	SAS	South Asian Ancestry	BEB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03606	male	SAME1840248	BEB	Bengali	SAS	South Asian Ancestry	BEB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03616	female	SAME1839955	BEB	Bengali	SAS	South Asian Ancestry	BEB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03642	female	SAME1839627	STU	Tamil	SAS	South Asian Ancestry	STU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03644	male	SAME1839638	STU	Tamil	SAS	South Asian Ancestry	STU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03646	male	SAME1839643	STU	Tamil	SAS	South Asian Ancestry	STU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03718	male	SAME1839834	ITU	Telugu	SAS	South Asian Ancestry	ITU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03720	male	SAME1839562	ITU	Telugu	SAS	South Asian Ancestry	ITU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03721	female	SAME1839659	ITU	Telugu	SAS	South Asian Ancestry	ITU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38
HG03722	female	SAME1839664	ITU	Telugu	SAS	South Asian Ancestry	ITU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
HG03890	male	SAME1839864	STU	Tamil	SAS	South Asian Ancestry	STU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA06991	female	SAME124936	CEU	CEPH	EUR	European Ancestry	CEU	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA06993	male	SAME124934	CEU	CEPH	EUR	European Ancestry	CEU	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA06994	male	SAME124931	CEU	CEPH	EUR	European Ancestry	CEU	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA06997	female	SAME124930	CEU	CEPH	EUR	European Ancestry	CEU	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA18484	female	SAME124101	YRI	Yoruba	AFR	African Ancestry	YRI	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA18485	male	SAME124100	YRI	Yoruba	AFR	African Ancestry	YRI	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA18486	male	SAME124099	YRI	Yoruba	AFR	African Ancestry	YRI	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA18488	female	SAME124103	YRI	Yoruba	AFR	African Ancestry	YRI	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA18525	female	SAME124672	CHB	Han Chinese	EAS	East Asian Ancestry	CHB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA18526	female	SAME124673	CHB	Han Chinese	EAS	East Asian Ancestry	CHB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,90 Han Chinese high coverage genomes
NA18530	male	SAME124484	CHB	Han Chinese	EAS	East Asian Ancestry	CHB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA18546	male	SAME124263	CHB	Han Chinese	EAS	East Asian Ancestry	CHB	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA18939	female	SAME123041	JPT	Japanese	EAS	East Asian Ancestry	JPT	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,Human Genome Structural Variation Consortium, Phase 2,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA18941	female	SAME124311	JPT	Japanese	EAS	East Asian Ancestry	JPT	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA18943	male	SAME124309	JPT	Japanese	EAS	East Asian Ancestry	JPT	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA18944	male	SAME124314	JPT	Japanese	EAS	East Asian Ancestry	JPT	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19017	female	SAME124259	LWK	Luhya	AFR	African Ancestry	LWK	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA19019	female	SAME124000	LWK	Luhya	AFR	African Ancestry	LWK	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA19020	male	SAME124855	LWK	Luhya	AFR	African Ancestry	LWK	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19025	male	SAME124852	LWK	Luhya	AFR	African Ancestry	LWK	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA19648	female	SAME123307	MXL	Mexican Ancestry	AMR	American Ancestry	MXL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19649	male	SAME123442	MXL	Mexican Ancestry	AMR	American Ancestry	MXL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19650	male	SAME124976	MXL	Mexican Ancestry	AMR	American Ancestry	MXL	1000 Genomes 30x on GRCh38,Human Genome Structural Variation Consortium, Phase 2,1000 Genomes phase 3 release
NA19651	female	SAME123123	MXL	Mexican Ancestry	AMR	American Ancestry	MXL	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19700	male	SAME124233	ASW	African Ancestry SW	AFR	African Ancestry	ASW	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19701	female	SAME124232	ASW	African Ancestry SW	AFR	African Ancestry	ASW	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA19702	male	SAME124231	ASW	African Ancestry SW	AFR	African Ancestry	ASW	1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA19704	female	SAME124236	ASW	African Ancestry SW	AFR	African Ancestry	ASW	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release
NA20502	female	SAME124358	TSI	Toscani	EUR	European Ancestry	TSI	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA20503	female	SAME124357	TSI	Toscani	EUR	European Ancestry	TSI	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA20509	male	SAME124354	TSI	Toscani	EUR	European Ancestry	TSI	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,Human Genome Structural Variation Consortium, Phase 2,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA20510	male	SAME124562	TSI	Toscani	EUR	European Ancestry	TSI	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release,1000 Genomes phase 1 release,Geuvadis
NA20845	male	SAME123430	GIH	Gujarati	SAS	South Asian Ancestry	GIH	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA20853	female	SAME123243	GIH	Gujarati	SAS	South Asian Ancestry	GIH	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA20854	female	SAME123248	GIH	Gujarati	SAS	South Asian Ancestry	GIH	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release
NA20858	male	SAME123207	GIH	Gujarati	SAS	South Asian Ancestry	GIH	1000 Genomes on GRCh38,1000 Genomes 30x on GRCh38,1000 Genomes phase 3 release