Large-Scale Genomics (LSG) Work Stream

Overview

Genomic sequencing generates data at an increasingly large scale. As public and national health systems continue to adopt genomic testing and more private companies launch genomic projects, the vast quantity of raw sequencing data will only balloon further. The Large-Scale Genomics (LSG) Work Stream has built and maintained robust, standardised ways to describe, store, and access this vital genomic information.

As part of a larger effort to adapt GA4GH to meet the evolving field of genomics, the Large-Scale Genomics Work Stream is now retired and its portfolio integrated into other existing GA4GH Work Streams. You may now find information about its products in the following places:

File Formats (Genomic Knowledge Standards Work Stream)
Whole Genome Sequencing Quality Control Standards (Genomic Knowledge Standards Work Stream)
Future of VCF (Genomic Knowledge Standards Work Stream)
Refget (Federated Analysis Work Stream)
Refget Sequence Collections (Federated Analysis Work Stream)
Htsget (Federated Analysis Work Stream)
Crypt4GH (Data Security Work Stream)

Announcements

Date	Title
6 March 2026	Join the next GIF “Ask Me Anything" event featuring Crypt4GH on 31 March!
13 November 2025	The Global Alliance for Genomics and Health (GA4GH) Product Steering Committee has approved the release of two new GA4GH products: Experiments Metadata Checklist and Whole Genome Sequencing Quality Control Standards
14 July 2025	Two GA4GH products are now open for public comment!
27 March 2025	The Global Alliance for Genomics and Health (GA4GH) Product Steering Committee has approved the release of two new GA4GH products: refget Sequence Collections and Variation Representation Specification (VRS) v2.0.
13 August 2024	Large Scale Genomics (LSG) Work Stream Crypt4GH survey is now available
6 August 2024	VCF v4.5 is now live!
29 February 2024	Refget: Sequence Collections v1.0 Open for Public Comment
17 July 2023	refget v2.0 approved
12 May 2023	Welcome to the new GA4GH website!
15 February 2023	GA4GH products open for comment: CRAM v3.1, refget v2.0
27 October 2022	Open for comment: Variant Summary Statistics Format v1.0

Publications Documents Videos

Publications

Title	Author(s)	Year
Rakeiora Genomics Platform: a pathfinder for genomic medicine research in Aotearoa New Zealand	Rye, C.E. et al. Rye, C.E., Puketapu-Watson, H., Wihongi, H., Te Aika, B., de Ligt, J., Print, C.G., Tsai, P., Curran, B., Jones, N., Huh, J, Owen Perkins, E., Pestle, M., Zhao, K., Halytskyy, Y., Robertson, S.P., Halliday, B.J., Goodin, E., Markie, D.M., Lamont, A., Wilcox, P.	2025
CRAM 3.1: advances in the CRAM file format	Bonfield, J.K. Bonfield, J.K.	2022
Refget: standardized access to reference sequences	Yates, A.D. et al. Yates, A.D., Adams, J., Chaturvedi, S., Davies, R.M., Laird, M., Leinonen, R., Nag, R., Sheffield, N.C., Hofmann, O., Keane, T.O.	2021
Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases	Corvò, A. et al. Corvò, A., Matalonga, L., Spalding, D., Senf, A., Laurie, S., Picó-Amador, D., Paramonov, I., Foix Romero, A., Garcia-Rios, E., Izquierdo Ciges, J,, Mohan, A., Thomas, C., Halmagyi, C., Freeberg, M.A., Töpf, A., Horvath, R., Saunders, G., Gut, I., Keane, T., Piscia, D., Beltran, S.	2020
End-to-End Security for Local and Remote Human Genetic Data Applications at the EGA	Senf, A. Senf, A.	2019
Htsget: A protocol for securely streaming genomic data	Kelleher, J. et al. Kelleher, J., Lin, M., Albach, C.H., Birney, E., Davies, R., Gourtovaia, M., Glazer, D., Gonzalez, C.Y., Jackson, D.K., Kemp, A., Marshall, J., Nowak, A., Senf, A., Tovar-Corona, J.M., Vikhorev, A., Keane, T.M.	2018
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes	Krusche, P. et al. Krusche, P., Trigg, L., Boutros, P.C., Mason, C.E., De La Vega, F.M., Moore, B.L., Gonzalez-Porta, M., Eberle, M.A., Tezak, Z., Lababidi, S., Truty, R., Asimenos, G., Funke, B., Fleharty, M., Salit, M., Zook, J.M.	2018
The variant call format and VCFtools		2011
Efficient storage of high throughput DNA sequencing data using reference-based compression		2011
The Sequence Alignment/Map format and SAMtools	Li, H. et al. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R.	2009

Documents

Date	Title
29 April 2026	GA4GH Implementation Forum (GIF) Ask Me Anything: Crypt4GH
17 September 2025	TASC Technical Specification Development 10.59756/tp-w574-4d
27 August 2024	GA4GH Updates Report — August 2024
24 May 2024	Meeting report: April Connect 2024
7 November 2023	Meeting Report: September Connect 2023
19 September 2023	GA4GH Product Development and Approval Process
14 September 2023	Code of Ethics and Community Conduct (CECC)
14 September 2023	Guidelines for respectful engagement
14 September 2023	Procedures for reviewing reported violations of the Code of Ethics and Community Conduct
5 April 2023	Informational packet: getting involved with GA4GH
11 March 2023	Meeting minutes: Crypt4gh
11 March 2023	Meeting minutes: File Formats
11 March 2023	Meeting minutes: Future of VCF
11 March 2023	Meeting minutes: Htsget
11 March 2023	Meeting minutes: Refget
11 March 2023	Meeting minutes: RNAget
10 March 2023	Start-up guide: refget
6 March 2023	Meeting minutes: Quality Control of Whole Genome Sequencing
6 March 2023	Road map: Quality Control of Whole Genome Sequencing
25 September 2022	Meeting minutes: Large-Scale Genomics
4 January 2022	Meeting minutes: crypt4gh (2022)
4 January 2022	Meeting minutes: RNASeq (2022)
12 December 2020	Meeting minutes: LSG — htsget (2021 to 2022)
8 December 2020	Meeting minutes: crypt4gh (2021)
8 December 2020	Meeting minutes: File Formats (2021)
8 December 2020	Meeting minutes: Future of VCF (2021)
8 December 2020	Meeting minutes: refget (2021)
8 December 2020	Meeting minutes: RNASeq (2021)
26 April 2019	CRAM: the genomics compression standard

Videos

	Date	Title
	24 September 2020	GA4GH 8th Plenary: Large-Scale Genomics Work Stream 2020 Updates
	25 March 2019	CRAM: the data storage standard of genomics
	25 March 2019	What is CRAM? \| James Bonfield
	22 March 2019	CRAM: a community effort
	5 December 2018	Using the GA4GH toolkit: htsget streaming API for genomic data
	5 December 2018	Using the GA4GH toolkit: refget API for retrieving reference sequences via checksum