bamtag: Outputs a tag to identify duplicate reads in GRanges input

In mskilab/bamUtils: Utility functions for manipulating BAMs

Outputs a tag to identify duplicate reads in GRanges input

Description

Outputs a tag that cats 'qname', first vs first second mate +/- secondary alignment +/- gr.string to give an identifier for determine duplicates in a read pile

Usage

bamtag(reads, secondary = FALSE, gr.string = FALSE)

Arguments

reads	GenomicRanges or GappedAlignments or data.frame holding the reads
secondary	boolean including secondary alignment(s) (default = FALSE)
gr.string	boolean input reads into gr.string() (default = FALSE)

mskilab/bamUtils documentation built on Sept. 28, 2022, 3:45 p.m.