GLIMPSE1

Genotype Likelihoods IMputation and PhaSing mEthod

Version 1

27/11/2022: This page describes the GLIMPSE1 method. GLIMPSE1 is recommended to the users who want to use the joint model, for imputation of >1x data and a moderate sized reference panels. For large reference panels and lower coverages, we recommend the use of the GLIMPSE2 method

GLIMPSE1 is a phasing and imputation method for large-scale low-coverage sequencing studies.

Main features of the method:

  1. Accurate imputed genotype calls. Our method takes advantage of reference panels to produce high quality genotype calls.
  2. Accurate phasing. GLIMPSE1 outputs accurate phased haplotypes for the low-coverage sequenced dataset.
  3. Low-coverage sequencing outperforms SNP arrays. Imputation using low-coverage sequencing data is competitive to SNP array imputation. Results for European and African-American populations are interactively available on the website.
  4. A cost-effective paradigm. GLIMPSE1 realises whole genome imputation from the HRC reference panel for less than 1$.
  5. An easy-to-use framework for diploid, haploid and mixed ploidy imputation. Our method is able to perform imputation of samples with different ploidy without the need to split the data.

GLIMPSE1 is available under the MIT licence on the Github repository https://github.com/odelaneau/GLIMPSE.


If you use the GLIMPSE1 in your research work, please cite the following paper:

Simone Rubinacci, Diogo Ribeiro, Robin Hofmeister, Olivier Delaneau. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nature Genetics 53.1 (2021): 120-126.


GLIMPSE1 is developed by Simone Rubinacci and Olivier Delaneau at the University of Lausanne, Switzerland.


GLIMPSE1 tools

GLIMPSE1 chunk

Version 1.1.1

Defines chunks where to run phasing and imputation.

Documentation

GLIMPSE1 phase

Version 1.1.1

Performs phasing and imputation refining genotype likelihoods.

Documentation

GLIMPSE1 ligate

Version 1.1.1

Concatenates chunks ligating phased information.

Documentation

GLIMPSE1 sample

Version 1.1.1

Generates haplotype calls by sampling haplotypes.

Documentation

Dashboard

21/05/2021: Version 1.1.1 is available on Github! An updated version of GLIMPSE1 is now available!
07/01/2021: The manuscript describing GLIMPSE1 is now published in Nature Genetics!
07/10/2020: Version 1.1.0 is available on Github! An updated version of GLIMPSE1 designed for diploid/haploid/mixed ploidy imputation is now available!
07/10/2020: A tutorial for non-PAR chrX imputation is now available! Click here to check it out!
07/10/2020: A tutorial for GRCh37/hg19 assembly is now available! Click here!
15/04/2020: Version 1.0.0 is available on Github! Check our Github page to download version 1.0.0 and have a GLIMPSE1 of your data
03/04/2020: A tutorial for GRCh38/hg38 build is now available. Click here to start running GLIMPSE1.
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