BEDPE

BEDPE file format:

Heading	Type	Description
chr1	String	Chromosome of lower coordinate
start1	0-based int	Start coordinate of lower coordinate
end1	1-based int	End coordinate of lower coordinate
chr2	String	Chromosome of high coordinate
start2	0-based int	Start coordinate of high coordinate
end2	1-based int	End coordinate of high coordinate
id/name	String	ID of event, correlates with VCF
brass_score	int	Number of aberrant pairs contributing to the rearrangement group.
strand1	[+-]	Strand of end in 'genomic' context - see table
strand2	[+-]	Strand of end in 'genomic' context - see table
sample	String	Name of sample as found in BAM RG header SM field, each sample contibuting will be listed.
svclass	String	Basic event type: deletion, inversion, tandem-duplication, translocation
bkdist	int	Distance between inner edges of breakpoints (-1 if difference chromosomes)
assembly_score	int	0-100, A "niceness" score for the Velvet assembly graph. A score of 100 indicates a perfect graph with five vertices forming a quintet. Points are deducted for isolated vertices, cruft hanging off the quintet, and major points for extra cycles and large-scale graph cruftiness.
readpair names	String	CSV of read pair names found in aberrant pair grouping (reads with mapping quality MPQ >= 6 )
readpair count	int	Count of read pair found in aberrant pair grouping (analogous to brass_score)
bal_trans	String	ID of event that describes reciprocal balanced translocation event
inv	String	ID of event that describes reciprocal inversion event
occL	int	Count of events that share lower coordinate (chr/start/end1) within 500 bp window
occH	int	Count of events that share higher coordinate (chr/start/end2) within 500 bp window
copynumber_flag	char	Indicate presence of copynumber change point from ASCAT NGS result
range_blat	int	flag indicating the degree of homology between the two sides of the breakpoint. For small distances this will always be high, since a region is being compared against itself. Range_blat filtering should therefore not be used in isolation. If needed range_blat can be required to be less than 100, as long as distance is greater than 1000
Brass Notation	String	A string containing the brass description of the break point - see table at end
non-template	String	Non templated sequence
micro-homology	String
assembled readnames	String	CSV of all individual reads that formed part of the ALT assembly path.
gene		Gene affected by disruption of the coding direction
gene_id		ID of gene affected by disruption of the coding direction
transcript_id		transcript ID affected by disruption of the coding direction
strand		Coding strand of affected feature
phase		Phase of breakpoint in affected feature
region
region_number
total_region_count
first/last		First or last element of exon structure.
fusion_flag		See BEDPE - Fusion-flag.

Strand1/2

SV Type	Strand (1/2)
Inversion	+/-
Inversion	-/+
Deletion	+/+
Tandem Dup.	-/-

BRASS notation

Paired-flag	Lower chr	Lower breakpoint	Higher chr	Higher breakpoint	NTS	Microhomology	Phase II output
4	4	114974732	4	115115727	-	G	Chr.4- 114974733(32)--G--115115728(27) Chr.4- (score 94)
8	6	126370389	6	134006924	GGCAAATATACTCTT	-	Chr.6- 126370389] GGCAAATATACTCTT [134006924 Chr.6 (score 95)
32	1	241559717	12	132126269	-	-	Chr.1- 241559717][132126269 Chr.12 (score 90)

Incomplete alignment for query to target assembly

When the assembled reads do not completely match the ends of the reference based target additional notation is added to the Chr.X elements of the 'Phase II output':

Chr.17  290000(200)--NNN--1350000(44)  Chr.17[@17]  (score 75)
Chr.3  186000000] NNN [11600000  Chr.16-[@651]  (score 94)

This denotes where the divergence occurs, if considered the low end (internally) the value is the point the query starts to match. If the high end (internally) it is the point the query starts to diverge. Scores are adjusted accordingly.