plink_rm_long_indels: Remove very long INDELS
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

Uses cut, sort, uniq and awk to find very long INDELS causing PLINK to be very memory hungry during analyses and excludes them using PLINK.

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plink_rm_long_indels(bfile, output.prefix, max_length, ...,
  bed.file = NULL, bim.file = NULL, fam.file = NULL,
  exec = "plink2", num.threads, memory)

`bfile`	[`string`] The basename of the binary PLINK files.
`output.prefix`	[`string`] The basename of the new binary PLINK files.
`max_length`	[`integer`] The maximum length of any allele.
`...`	[`character`] Additional arguments passed to PLINK.
`bed.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`bim.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`fam.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`exec`	[`string`] Path of PLINK executable.
`num.threads`	[`int`] Number of CPUs usable by PLINK. Default is determined by SLURM environment variables and at least 1.
`memory`	[`int`] Memory for PLINK in Mb. Default is determined by minimum of SLURM environment variables `SLURM_MEM_PER_NODE` and `num.threads * SLURM_MEM_PER_CPU` and at least 5000.