This function takes a phased Beagle output and rewrites the output.
subPhased(file=NULL, vmmk = NULL, out=NULL, chunkSize=100000, verbose=TRUE,
removeInsertions=TRUE)Location of the original Beagle file (String).
Location of the Variant Map Master key (String).
Name and location of the output file (String).
For large Beagle files, the chunk size.
The function gives feedback.
All Indels will be removed.
A rewritten beagle phased file.
This function takes a Beagle phased file and rewrites the alleles from numerical to character, based on the information provided in a variant map master key. For larger files the function can process the rewriting in chunks in order to save memory.