loose.reads2: loose.reads2

In mskilab/loosends: Classifying loose ends in gGraphs

loose.reads2

Description

Performs the following:

• loads reads from a specified window around loose end

• identifies any split reads and loads the "sides" of those reads as well

• loads the mates of reads around the loose end (by qname)

• realigns all of these reads

The supplied BAM files are expected to have tag SA (indicated split alignments) The functionality is identical to loose.reads; however, the BAMs are expected to be prefiltered to contain only the relevant QNAMEs via samtools to avoid slow filtering in R for reads with many mate windows

Usage

loose.reads2(
  tbam,
  taln,
  nbam = NA,
  naln = NA,
  id = "",
  filter = FALSE,
  verbose = FALSE
)

Arguments

tbam	(character) path to tumor BAM file
taln	(character) path realigned tumor bam
nbam	(character) optional, path to normal BAM file, default=NULL
naln	(character) optional, realigned normal bam
id	(character)
filter	(logical) return loose read pairs only? default FALSE
verbose	optional, default=FALSE

Value

data.table of reads relaigned to the specified reference

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.