Na klasteru je dostupan programski paket PLINK. Informacije o samom programu mogu se pronaći na službenoj stranici.
PLINK tool set is available for user. More info on how to run this tool set can be found on official web pages.
How to use:
Available versions and modules:
| Version | Module |
|---|---|
| 1.9 | bioinfo/plink/1.9 |
Example data can be downloaded from https://zzz.bwh.harvard.edu/plink/tutorial.shtml
To use more then one thread you must use a mpisingle parallel environment as plink is not able to use more than one node. In this case you need to make sure plink uses the same number of threads as you requested. In this example we use $NSLOTS variable for this:
Primjer pokretanja
#!/bin/bash/ #$ -N test_plink #$ -cwd #$ -pe *mpisingle 5 module load plink/1.9 plink --file hapmap1 --threads $NSLOTS plink --file hapmap1 --make-bed --out hapmap1 --threads $NSLOTS plink --file hapmap1 --make-bed --mind 0.05 --out highgeno --threads $NSLOTS plink --bfile hapmap1 --missing --out miss_stat --threads $NSLOTS plink --bfile hapmap1 --chr 1 --out res1 --missing --threads $NSLOTS plink --bfile hapmap1 --chr 2 --out res2 --missing --threads $NSLOTS plink --bfile hapmap1 --freq --out freq_stat --threads $NSLOTS plink --bfile hapmap1 --freq --within pop.phe --out freq_stat --threads $NSLOTS plink --bfile hapmap1 --snp rs1891905 --freq --within pop.phe --out snp1_frq_stat --threads $NSLOTS plink --bfile hapmap1 --assoc --out as1 --threads $NSLOTS sort --key=7 -nr as1.assoc | head plink --bfile hapmap1 --assoc --adjust --out as2 --threads $NSLOTS plink --bfile hapmap1 --pheno pop.phe --assoc --adjust --out as3 --threads $NSLOTS plink --bfile hapmap1 --model --snp rs2222162 --out mod1 --threads $NSLOTS plink --bfile hapmap1 --model --cell 0 --snp rs2222162 --out mod2 --threads $NSLOTS plink --bfile hapmap1 --cluster --mc 2 --ppc 0.05 --out str1 --threads $NSLOTS plink --bfile hapmap1 --mh --within str1.cluster2 --adjust --out aac1 --threads $NSLOTS plink --bfile hapmap1 --cluster --cc --ppc 0.01 --out version2 --threads $NSLOTS plink --bfile hapmap1 --mh --within version2.cluster2 --adjust --out aac2 --threads $NSLOTS plink --bfile hapmap1 --cluster --K 2 --out version3 --threads $NSLOTS plink --bfile hapmap1 --mh --within pop.phe --adjust --out aac3 --threads $NSLOTS plink --bfile hapmap1 --cluster --matrix --out ibd_view --threads $NSLOTS