The LTSOFT application implements a new approach to using information from known associated variants when conducting disease association studies. The approach is based in part on the classical technique of liability threshold modeling and performs estimation of model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature.

References:

• Noah Zaitlen, Bogdan Pasaniuc, Nick Patterson, et al.,
  Analysis of case–control association studies with known risk variants
  BioinformaticsVolume 28, Issue 13, July 2012, Pages 1729–1737, https://doi.org/10.1093/bioinformatics/bts259.
• Noah Zaitlen, Sara Lindstrom, Bogdan Pasaniuc, et al.,
  Informed Conditioning on Clinical Covariates Increases Power in Case-Control Association Studies
  PLOS GeneticsNovember 2012 | Volume 8 | Issue 11 | e1003032.

• LTSOFT Home page

• Module Name: ltsoft (see the modules page for more information)
• Unusual environment variables set
  • LTSOFT_HOME  installation directory
  • LTSOFT_BIN       executable directory
  • LTSOFT_SRC       source code directory
  • LTSOFT_DATA  sample data directory

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

[user@biowulf]$ sinteractive 
[user@cig 3335 ~]$ module load ltsoft
[+] Loading singularity  3.10.5  on cn4326
[+] Loading ltsoft  4.0
[user@cn4326 ~]$ ls $LTSOFT_BIN
convertf  gcta64  ltfit  LTFIT  LTMLM  ltprev  ltpub  ltscore  LTSCORE  ltscore.perl 
[user@cn4326 ~]$ ltfit
usage:  ltfit  < parameter-file >
[user@cn4326 ~]$ ltprev
usage:  ltprev < parameter-file >
[user@cn4326 ~]$ ltpub
usage: ltpub < in-file > < outfile >
[user@cn4326 ~]$ ltscore
usage:  ltscore 
[user@cn4326 ~]$ ltscore.perl --help
...

Usage: ltscore.perl [-OPTIONS [-MORE_OPTIONS]] [--] [PROGRAM_ARG1 ...]

The following single-character options are accepted:
        With arguments: -g -i -n -c -o -s -p

Options may be merged together.  -- stops processing of options.
Space is not required between options and their arguments.
...