runAnchoredFusion: runAnchoredFusion
In zhangbaifeng/SplitFusion: Detection of gene fusion based on split alignments

Description Usage Arguments Details Examples

Main function of AnchoredFusion software.

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

`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).

(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.

1 2	runSplitFuion(step = c("bam-consolidate", "breakpoint-consolidate", "breakpoint-filter"), configFile = "/path/example.configFile", output = "/path/result", sample.id = "example")