AlleleProfileR.map: Align reads to the reference genome

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

Align the reads to the reference using BWA. This external software needs to be installed manually and needs to be addressable from the terminal.

Usage

AlleleProfileR.map(files, method = "bwa", index, subset = NULL)

Arguments

files	Vector with files. Output of AlleleProfileR.read.folders
method	Mapping method, default is BWA (BWA-MEM).
index	Path to the .fa file containing the reference genome.
subset	Vector with the indices of the entries that should be processed. Default is NULL, all entries will be analyzed.

Author(s)

Arne Bruyneel

References

• Li, H. and Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010;26(5):589-595.

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.