Convert DArTseqLD reports to VCF

This function converts a dual-file report format that we (NextGen Cassava Breeding) have arranged with DArT.

convertDart2vcf(
  dartvcfInput,
  dartcountsInput,
  outName,
  nskipvcf = 2,
  nskipcounts = 3,
  ncores
)

Value

The output of this step is written to disk as a *.vcf.gz completely compatible with downstream bioinformatics softwares!

Details

The output of this step is written to disk as a *.vcf.gz completely compatible with downstream bioinformatics softwares!

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: convertVCFtoDosage(), createGenomewideDosage(), filter_positions(), mergeVCFs(), postImputeFilterBeagle4pt1(), postImputeFilter(), runBeagle4pt1GL(), runBeagle5(), splitVCFbyChr()