Subset a VCF file based on provided positions

Uses vcftools --positions

filter_positions(inPath = NULL, inVCF, positionFile, outPath = NULL, outName)

Arguments

positionFile

see VCFtools

outName

Value

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(), mergeVCFs(), postImputeFilterBeagle4pt1(), postImputeFilter(), runBeagle4pt1GL(), runBeagle5(), splitVCFbyChr()