subPhased {hoardeR}

Rewrite the Phased File from a Beagle Output

Description

This function takes a phased Beagle output and rewrites the output.

Usage

  subPhased(file=NULL, vmmk = NULL, out=NULL, chunkSize=100000, verbose=TRUE,
            removeInsertions=TRUE)

Arguments

file

Location of the original Beagle file (String).

vmmk

Location of the Variant Map Master key (String).

out

Name and location of the output file (String).

chunkSize

For large Beagle files, the chunk size.

verbose

The function gives feedback.

removeInsertions

All Indels will be removed.

Details

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.

Value

A rewritten beagle phased file.

Author(s)

Daniel Fischer