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GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies. It perform accurate imputed genotype calls and outperforms SNP arrays.

References:

• S. Rubinacci, D.M. Ribeiro, R. Hofmeister, O. Delaneau
  Efficient phasing and imputation of low-coverage sequencing data using large reference panels
  bioRxiv preprint doi: https://doi.org/10.1101/2020.04.14.040329;

• GLIMPSE Home page

• Module Name: GLIMPSE (see the modules page for more information)
• Unusual environment variables set
  • GLIMPSE_HOME  installation directory
  • GLIMPSE_BIN       executable directory
  • GLIMPSE_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=16g --cpus-per-task=16
[user@cn3335 ~]$module load GLIMPSE
[+] Loading GLIMPSE  1.1.1

[user@biowulf]$ GLIMPSE_chunk 

[GLIMPSE] Split chromosomes into chunks
  * Author        : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne
  * Contact       : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch
  * Version       : 1.1.1
  * Run date      : 21/11/2022 - 17:25:19
...
[user@biowulf]$ GLIMPSE_ligate 
...
[user@biowulf]$ GLIMPSE_sample
...
[user@biowulf]$ GLIMPSE_concordance
...
[user@biowulf]$ GLIMPSE_phase
...
[user@biowulf]$ GLIMPSE_snparray
...

[user@cn3335 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$