jJ: parse junctions from a variety of formats
In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

jJ	R Documentation

parse junctions from a variety of formats

Description

Parsing various formats of structural variation data into junctions.

Usage

jJ(rafile,
keep.features = T,
seqlengths = NULL,
chr.convert = T,
geno=NULL,
flipstrand = FALSE,
swap.header = NULL,
breakpointer = FALSE,
seqlevels = NULL,
force.bnd = FALSE,
skip = NA)

Arguments

`rafile`	path to the junctions file. See details for the compatible formats.
`keep.features`	`logical`, if TRUE preserve meta data from the input
`seqlengths`	a named `numeric` vector containing reference contig lengths
`chr.convert`	`logical`, if TRUE strip "chr" prefix from contig names
`geno`	`logical`, whether to parse the 'geno' fields of VCF
`hg`	`character`, human genome version
`flipstrand`	`logical`, if TRUE will flip breakpoint strand
`swap.header`	path to the alternative VCF header file
`breakpointer`	`logical`, if TRUE will parse as breakpointer output
`seqlevels`	vector for renaming the chromosomes
`force.bnd`	if TRUE overwrite all junction "type" to "BND"
`skip`	`numeric` lines to skip

Details

A junction is a unordered pair of strand-specific genomic locations (breakpoints). Within a given reference genome coordinate system, we call the direction in which coordinates increase "+". A breakpoint is a width 1 (start==end)genomic range with strand specified, and "+" means the side with larger coordinate is fused with the other breakpoint in a junction.

rafile must be one of the following formats: 1) Some VCF (variant call format). We currently support the VCF output from a number of structural variation detection methods, namely SvABA (https://github.com/walaj/svaba), DELLY (https://github.com/dellytools/delly), LUMPY (https://github.com/arq5x/lumpy-sv), novoBreak (https://sourceforge.net/projects/novobreak/). In theory, VCF defined with BND style should be compatible but be cautious when using the output from other methods since no universal data definition is adopted by the community yet. 2) BEDPE (http://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) 3) Textual output from Breakpointer (http://archive.broadinstitute.org/cancer/cga/breakpointer) 4) R serialized object storing junctions (.rds)

Value

a Junction object

Warning

We assume the orientation definition in the input is consistent with ours. Check with the documentation of your respective method to make sure. If the contrary, use flipstrand=TRUE to reconcile.