runBeagle4pt1GL: Run Beagle4.1 to impute a target VCF with a reference VCF

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Run Beagle4.1 to impute a target VCF with a reference VCF

Description

Beagle4.1 is slower than Beagle5 by far. However, it can use genotype-likelihoods (the GL VCF field) for its algorithm, which is potentially more accurate. In cases like imputing GBS data, or if you have time to wait around, this should be better than Beagle5.0 for a first pass imputation of observed sites. Impute with Beagle V5.0. Use an "imputation reference panel". Refer to Beagle documentation for meaning of arguments passed.

Usage

runBeagle4pt1GL(
  targetVCF,
  refVCF,
  mapFile,
  outName,
  nthreads,
  maxmem = "500g",
  impute = TRUE,
  ne = 1e+05,
  samplesToExclude = NULL,
  niter = 10
)

Arguments

targetVCF	passes to Beagle 'gl=targetVCF'
refVCF	passes to Beagle 'ref=targetVCF'
mapFile	passes to Beagle 'map=mapFile'
outName	passes to Beagle 'out=outName (don't put file suffix, Beagle adds *.vcf.gz).
nthreads	passes to Beagle 'nthreads=nthreads'
maxmem	passes to java '-Xmx<maxmem>'
impute	passes to Beagle 'impute=TRUE'
ne	passes to Beagle 'ne=ne'
niter	passes to Beagle 'niterations=niter'

Details

NOTICE: This function is part of a family of functions ("imputation_functions") developed as part of the NextGen Cassava Breeding Project genomic selection pipeline. For some examples of their useage:

• IITA_2021GS (should be first use of this package)

• NRCRI_2021GS

• TARI_2020GS

See Also

Other imputation_functions: convertDart2vcf(), convertVCFtoDosage(), createGenomewideDosage(), filter_positions(), mergeVCFs(), postImputeFilterBeagle4pt1(), postImputeFilter(), runBeagle5(), splitVCFbyChr()

wolfemd/genomicMateSelectR documentation built on July 1, 2022, 10:42 p.m.