plink

Version:: 1.9b_6.21, 2.00a2.3, 2.00a3.6
Category:: bio
Cluster:: Vali

Author / Distributor

Description

PLINK is a widely-used open-source toolset for whole-genome association and population-based linkage analyses.

Key capabilities:

Genome-wide association studies (GWAS)
Population genetics and linkage analysis
Data management and format conversion
Variant filtering and quality control
Supports multi-threaded execution for performance

Note

PLINK provides two main versions: plink (1.9) and plink2 (2.0). Make sure to use the correct command based on the module loaded

Documentation

 > plink2 --help

 PLINK v2.00a2.3 AVX2 (24 Jan 2020)             www.cog-genomics.org/plink/2.0/
 (C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3

 plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]
 plink2 --help [flag name(s)...]

Most PLINK runs require exactly one main input fileset.  The following flags
are available for defining its form and location:

--pfile <prefix> ['vzs']  : Specify .pgen + .pvar[.zst] + .psam prefix.
--pgen <filename>         : Specify full name of .pgen/.bed file.
--pvar <filename>         : Specify full name of .pvar/.bim file.
--psam <filename>         : Specify full name of .psam/.fam file.

--bfile  <prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix.
--bpfile <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.

--keep-autoconv    : When importing non-PLINK-binary data, don't delete
                     autogenerated binary fileset at end of run.

--no-fid           : .fam file does not contain column 1 (family ID).
--no-parents       : .fam file does not contain columns 3-4 (parents).
--no-sex           : .fam file does not contain column 5 (sex).

--vcf <filename> ['dosage='<field>]
--bcf <filename> ['dosage='<field>]  (not implemented yet) :
  Specify full name of .vcf{|.gz|.zst} or BCF2 file to import.
  * These can be used with --psam/--fam.
  * By default, dosage information is not imported.  To import the GP field
    (must be VCFv4.3-style 0..1, one probability per possible genotype), add
    'dosage=GP' (or 'dosage=GP-force', see below).  To import Minimac3-style
    DS+HDS phased dosage, add 'dosage=HDS'.  'dosage=DS' (or anything else
    for now) causes the named field to be interpreted as a Minimac3-style
    dosage.
    Note that, in the dosage=GP case, PLINK 2 collapses the probabilities
    down to dosages; you cannot use PLINK 2 to losslessly convert VCF
    FORMAT:GP data to e.g. BGEN format.  To make this more obvious, PLINK 2
    now errors out when dosage=GP is used on a file with a FORMAT:DS header
    line and --import-dosage-certainty wasn't specified, since dosage=DS
    extracts the same information more quickly in this situation.  You can
    suppress this error with 'dosage=GP-force'.
    In all of these cases, hardcalls are regenerated from scratch from the
    dosages.  As a consequence, variants with no GT field can now be
    imported; they will be assumed to contain only diploid calls when HDS is
    also absent.

--data <filename prefix> [REF/ALT mode] ['gzs']
--bgen <filename> [REF/ALT mode] ['snpid-chr']
--gen <filename> [REF/ALT mode]
--sample <filename> :
  Specify an Oxford-format dataset to import.  --data specifies a .gen[.zst]
  + .sample pair, while --bgen specifies a BGEN v1.1+ file.
  * If a BGEN v1.2+ file contains sample IDs, it may be imported without a
    companion .sample file.
  * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field
    instead of the usual chromosome field.
  * The following REF/ALT modes are supported:
    'ref-first': The first allele for each variant is REF.
    'ref-last': The last allele for each variant is REF.
    'ref-unknown' (default): The last allele for each variant is treated as
                             provisional-REF.
    This parameter will be required instead of optional in alpha 3.

--haps <filename> [{ref-first | ref-last}]
--legend <filename> <chr code> :
  Specify .haps [+ .legend] file(s) to import.
  * When --legend is specified, it's assumed that the --haps file doesn't
    contain header columns.
  * On chrX, the second male column may contain dummy '-' entries.  (However,
    PLINK 2 currently cannot handle omitted male columns.)
  * If not used with --sample, new sample IDs are of the form 'per#/per#'.

Output files have names of the form 'plink2.<extension>' by default.  You can
change the 'plink2' prefix with

--out <prefix>     : Specify prefix for output files.

Examples/Usage

Load the PLINK module:

$ module load PLINK/2.00a2.3-GCC-10.3.0

Unload the module:

$ module unload PLINK/2.00a2.3-GCC-10.3.0

Start MATLAB with full desktop environment:
```
$ plink2
```

Serial Jobs

Here is an example job for PLINK version 1.9 running on 4 cores and 8GB of memory:

#!/bin/bash
#SBATCH -n 4               # (or --ntasks=4) Request 4 cores
#SBATCH --mem-per-cpu=2G   # Request 2GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load plink/1.9-beta6.27-gcc-12.2.0

plink --threads ${SLURM_NTASKS} \
      --silent \
      --dummy 387 1112 0.03 scalar-pheno \
      --out dummy1

plink --threads ${SLURM_NTASKS} \
      --bfile dummy1 \
      --recode \
      --out dummy1.new_recode

Here is an example job for PLINK version 2.0 running on 4 cores and 8GB of memory:

#!/bin/bash
#SBATCH -n 4               # (or --ntasks=4) Request 4 cores
#SBATCH --mem-per-cpu=2G   # Request 2GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load plink

plink2 --threads ${SLURM_NTASKS} \
      --dummy 387 1112 0.03 scalar-pheno \
      --out dummy1

plink2 --threads ${SLURM_NTASKS} \
      --pfile dummy1 \
      --export vcf \
      --freq \
      --keep-autoconv \
      --out dummy1.new_recode

Installation

PLINK is pre-installed on the cluster and available via modules. Load the appropriate module and use directly.