Biowulf High Performance Computing at the NIH
PREST on Biowulf

PREST is a program that detects pedigree errors by use of genome-screen data. PREST incorporates the EIBD, AIBS, IBS, and MLLR test statistics developed by McPeek and Sun. ALTERTEST is a program that performs the EIBD, AIBS, IBS and MLLR tests on the problematic relative pairs identified using PREST. The purpose of ALTERTEST is to allow the user to choose the relationship to be used as the null hypothesis for the tests, and this relationship is allowed to be different from that given by the pedigree. In contrast, PREST will automatically use the relationship specified by the pedigree as the null hypothesis for the tests. ALTERTEST can be used independently of PREST.

The current PREST distribution includes an R program written by Daniel E. Weeks that draws out the the sharing probabilities on the 'relationship triangle' as described in Elizabeth Thompson's book "Pedigree Analysis in Human Genetics".


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 input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load prest
[user@cn3144 ~]$ cp $PREST_EXAMPLES/ex_chr01.idx .
[user@cn3144 ~]$ cp $PREST_EXAMPLES/ex_chr01.ped .
[user@cn3144 ~]$ cp $PREST_EXAMPLES/ex_chromfiles .
[user@cn3144 ~]$ cp $PREST_EXAMPLES/ex_pedigrees .
[user@cn3144 ~]$ prest ex_pedigrees ex_chromfiles 2

R can be used to generate plots.

[user@cn3144 ~]$ module load R
[+] Loading gcc  7.2.0  ...
[+] Loading GSL 2.4 for GCC 7.2.0 ...
[+] Loading openmpi 3.0.0  for GCC 7.2.0
[+] Loading R 3.5.0_build2
[user@cn3144 ~]$ R

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
> source("/usr/local/apps/prest/3.02/prest.r")
> postscript(paper="letter",horizontal=F)
> prest("prest_out2")
> q()
Save workspace image? [y/n/c]: n
[user@cn3144 ~]$ ps2pdf
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$