PRIMUS stands for Pedigree Reconstruction (PR) and Identification of a Maximum Unrelated Set (IMUS).
The IMUS method is an algorithm adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated individuals, given a specified threshold of relatedness. Additional information for preferential selection of individuals may also be utilized.
The PR algorithm is a method to reconstruct pedigrees within a genetic dataset. PRIMUS can verify expected pedigree structures from genetic data, and it can identify and incorporate novel, cryptic relationships into pedigrees.
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 PRIMUS
[+] Loading plink 2.3-alpha
[+] Loading PRIMUS 1.9.0
[user@cn3144 ~]$ cp $PRIMUS_TEST_DATA/complete.genome .
[user@cn3144 ~]$ run_PRIMUS.pl --plink complete.genome
FILES AND COLUMNS
LOG FILE: complete.genome_PRIMUS/PRIMUS_output.log
IBD file: complete.genome (FID1=1; IID1=2; FID2=3; IID2=4; IBD0=7; IBD1=8; IBD2=9; PI_HAT/RELATEDNESS=10)
Dataset results dir: complete.genome_PRIMUS
Age file: none
Sex file: none
Affection file: none
Trait weighting:
size (size)
SETTINGS
Get PLINK IBD ESTIMATES with prePRIMUS: 0
Automatic reference population selection: 1
Verbose: 1
Relatedness threshold: 0.09375
Initial likelihood cutoff: 0.3
Max generations: none
Max generational mating gap: 0
Get max unrelated set: 1
Reconstruct pedigrees: 1
Relatedness_file: complete.genome
Threshold: 0.09375
Selection criteria are based on the following:
size (size)
IDENTFYING FAMILY NETWORKS IN DATA
Writing network files to complete.genome_PRIMUS/
Loading data...
done.
done.
IDENTIFYING A MAXIMUM UNRELATED SET
Checking for large networks...
done.
# of family networks: 1
Writing out unrelated set
done.
Testing alternative methods...
done.
unrelated_file: complete.genome_maximum_independent_set
unrelated_set size: 6
RECONSTRUCTING complete.genome_network1
Output directory: complete.genome_PRIMUS/complete.genome_network1
Use mito non-match: 0
Use mito match: 0
Use Y non-match: 0
Use Y match: 0
Entering Resolve PC trios. # of possible pedigrees: 1
Entering Phase 1. # of possible pedigrees: 1
Entering Phase 2. # of possible pedigrees: 1
Entering Phase 3. # of possible pedigrees: 1
networks pre-prune: 1
networks post-prune: 1
Writing summary file
Writing .fam file for complete.genome_network1_1
Writing dataset Summary file complete.genome_PRIMUS/Summary_complete.genome.txt
done.
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$
Create a batch input file (e.g. PRIMUS.sh). For example:
#!/bin/bash set -e module load PRIMUS run_PRIMUS.pl --plink input.genome
Submit this job using the Slurm sbatch command.
sbatch [--mem=#] PRIMUS.sh
Create a swarmfile (e.g. PRIMUS.swarm). For example:
run_PRIMUS.pl --plink input1.genome run_PRIMUS.pl --plink input2.genome run_PRIMUS.pl --plink input3.genome run_PRIMUS.pl --plink input4.genome
Submit this job using the swarm command.
swarm -f PRIMUS.swarm [-g #] --module PRIMUSwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| --module PRIMUS | Loads the PRIMUS module for each subjob in the swarm |