GLIMPSE

Genotype Likelihoods IMputation and PhaSing mEthod

Catch a glimpse of your low depth sequencing data

GLIMPSE 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. GLIMPSE 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. GLIMPSE 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.

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


If you use the GLIMPSE 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.


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


GLIMPSE tools

GLIMPSE chunk

Version 1.1.0

Defines chunks where to run phasing and imputation.

Documentation

GLIMPSE phase

Version 1.1.0

Performs phasing and imputation refining genotype likelihoods.

Documentation

GLIMPSE ligate

Version 1.1.0

Concatenates chunks ligating phased information.

Documentation

GLIMPSE sample

Version 1.1.0

Generates haplotype calls by sampling haplotypes.

Documentation

Dashboard

07/10/2020: Version 1.1.0 is available on Github! An updated version of GLIMPSE 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 GLIMPSE of your data
03/04/2020: A tutorial for GRCh38/hg38 build is now available. Click here to start running GLIMPSE.
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