runAnchoredFusion: runAnchoredFusion

In Zheng-NGS-Lab/SplitFusion: Detection of gene fusion based on split alignments

runAnchoredFusion

Description

Main function of AnchoredFusion software.

Usage

runAnchoredFusion(step = c("bam-consolidate", "breakpoint-consolidate",
  "breakpoint-filter", "breakpoint-anno", "breakpoint-anno-post"), configFile,
  output, sample.id)

Arguments

step	step name in which you want to run AnchoredFusion, included "bam-consolidate", "breakpoint-consolidate", "breakpoint-filter", "breakpoint-anno" and "breakpoint-anno-post" five steps.
configFile	config file which sets the path and parameters of depended tools.
output	directory of output.
sample.id	sample name (matches with prefixed name of raw fastq or bam file).

Details

(https://github.com/Zheng-NGS-Lab/AnchoredFusion/blob/master/README.md).

A fast pipeline for detection of gene fusion based on fusion-supporting split alignment.

Examples

runSplitFuion(step = c("bam-consolidate", "breakpoint-consolidate", "breakpoint-filter"),
configFile = "/path/example.configFile", output = "/path/result", sample.id = "example")

Zheng-NGS-Lab/SplitFusion documentation built on March 29, 2025, 11:01 a.m.