postImputeFilterBeagle4pt1: Apply quality filters after imputation by Beagle4.1

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Apply quality filters after imputation by Beagle4.1

Description

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

Usage

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

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()

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