WP4 / WP5 Use Case and Dataset Matrix

	A	B	C	D	E	F	G	H	I	J	K	L	M
1	Category	Attribute	GEUVADIS	CSC virtual cohort (GEUVADIS YRI individuals)	HipSci Open	EGAD00001003338	EGAD00001006308	CoLaus	Estonian Biobank	BIOS	GTEx	HipSci	Required?

2	General information	Access type	Open	Open	Open	Controlled	Controlled	Controlled	Controlled	Controlled	Controlled	Controlled	Y
3		Location	ENA/1000 Genomes FTP	CSC / local EGA	ENA	EGA Central	EGA Central	SIB	UTartu	EGA Central/UMCG	Google Cloud	EGA	Y
4		DAC contact information (e-mail, URL, dbGaP, etc)	NA	NA	NA	EGA Test DAC	EGA Test DAC	TBC	releases@ut.ee	https://www.bbmri.nl/acquisition-use-analyze/bios	dbGaP	datasharing@sanger.ac.uk	Y
5		cell type or tissue	LCL	LCL	iPSC			LCL	whole blood	whole blood	LCL, whole blood, others	iPSC	Y
6		imputation reference panel	NA	NA	not imputed	NA	NA	1KG Phase 1	NA	HRC	NA	not imputed	N
7		Phenotype data	N	N	N	In progress	Y	Y	Y	Y	N	N	N
8		Case / Control	N	N	N	TBC	Y	N	N	N	N	N	N
9		Case Only	Y	Y	Y	TBC	N	Y	Y	Y	Y	Y	N
10		Number of individuals	462	87	~200		2504	555	491	~2000	864	~200	Y
11		Number of samples	462	87	~200		2504	555	491	~2000	~18000	~200	Y
12		Controller				Dylan	Dylan
13		Additional links		https://github.com/CINECA-project/wp4-federated-joint-cohort-analysis/blob/master/virtual_cohort/GEUVADIS_YRI_samples.tsv
14	Genotype data	Genotype data available?	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y	Y
15		Genotype data format (VCF, PLINK, bgen, idat)	VCF	VCF	VCF	BAM, CRAM	VCF, PLINK	TBC	VCF	VCF	VCF	idat	Y
16		genotype reference genome	GRCh37/GRCh38	GRCh38	GRCh37	GRCh37	GRCh37	GRCh37	GRCh37	GRCh37	GRCh38	GRCh37	Y
17		genotype data type (array, WGS)	WGS	WGS	array	WGS	WGS	TBC	WGS	array	WGS	array	N
18	RNA-seq data	RNA-seq data available?	Y	Y	Y	TBC	TBC	Y	Y	Y	Y	Y	Y
19	RNA-seq data	RNA-seq data format (CRAM, BAM, FASTQ, SRA)	FASTQ	FASTQ	CRAM/BAM			BAM	FASTQ	FASTQ	CRAM	CRAM/BAM	Y
20	Data formats	BAM	N	N	Y	Y	N	Y	N	TBC	N	Y
21		CRAM	N	N	Y	Y	N	N	N	TBC	Y	Y
22		VCF	Y	Y	Y	TBC	Y	TBC	Y	TBC	Y	N
23		PLINK	N	N	N	TBC	Y	TBC	N	TBC	N	N
24	APIs and data access	htsget	N	N	Y	Y	Y	TBC	N	TBC	TBC	Y
25	APIs and data access	ELIXIR AAI	N/A (open access)	N/A (open access)	N/A (open access)	Y (by EGA)	Y (by EGA)			Y (by EGA)		Y (by EGA)
26	Applicability for use cases	Joint cohort genotyping	Yes	Yes	Yes	Yes	Yes	Genotyping format unknown	Yes	Yes	Yes	If there are no VCFs, won't work with IDAT
27		Polygenic risk score	No phenotypes	No phenotypes	No phenotypes	Yes	Yes	Yes	Yes	Yes	No phenotypes	No phenotypes
28		eQTL	Yes	Yes	Yes	TBC	TBC	Yes	Yes	Yes	Yes	Yes
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