runBeagle5: Run Beagle5 to impute a target VCF with a reference VCF

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Run Beagle5 to impute a target VCF with a reference VCF

Description

Impute with Beagle V5.0. Use an "imputation reference panel". Refer to Beagle documentation for meaning of arguments passed.

Usage

runBeagle5(
  targetVCF,
  refVCF,
  mapFile,
  outName,
  nthreads,
  maxmem = "500g",
  impute = TRUE,
  ne = 1e+05,
  samplesToExclude = NULL
)

Arguments

targetVCF	passes to Beagle 'gt=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'
samplesToExclude

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(), runBeagle4pt1GL(), splitVCFbyChr()

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