GLIMPSE: Genotype Likelihoods IMputation and PhaSing mEthod

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


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

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

[GLIMPSE] Split chromosomes into chunks
  * Author        : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne
  * Contact       : &
  * 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 ~]$