Apply quality filters after imputation by Beagle4.1

Remove markers from the imputed VCF based on adjustable thresholds. For VCFs imputed by Beagle4.1.

postImputeFilterBeagle4pt1(
  inPath = NULL,
  inName,
  outPath = NULL,
  outName,
  AR2thresh = 0.75,
  HWEthresh = 1e-20,
  MAFthresh = 0.005
)

Arguments

inPath

path to input VCFs

inName

imputed input VCF name

outPath

path for output to be written to

outName

name desired, don't add file suffix, will be *.vcf.gz

HWEthresh

remove if p-value HWE from vcftools --hardy less than threshold, smaller p-value means more departure from HWE

MAFthresh

remove if minor allele frequency less than threshold

DR2thresh

remove if imputation quality score DR2 supplied in the VCF INFO field by Beagle is less than or equal to the threshold

Value

Details

Uses vcftools and R. of minor allee frequency MAFthresh, p-value measuring likelihood of divergence from hardy-weinberg equilibrium ()

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(), postImputeFilter(), runBeagle4pt1GL(), runBeagle5(), splitVCFbyChr()