Breakdancer output (file format) - Revision history

WikiBot: {{Type link}} used

2013-05-17T09:39:08Z

{{Type link}} used

WikiBot: {{Type link}} used

2013-05-17T09:36:45Z

{{Type link}} used

WikiBot: Target element type added

2013-05-16T06:47:05Z

Target element type added

WikiBot: Plugin link added

2013-05-07T07:12:51Z

Plugin link added

WikiBot: Protected "Breakdancer output (file format)": Autogenerated page (‎[edit=sysop] (indefinite))

2013-04-04T09:28:17Z

Protected "Breakdancer output (file format)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Added 'Autogenerated pages' category

2013-04-04T09:28:16Z

Added 'Autogenerated pages' category

WikiBot: Automatic synchronization with BioUML

2013-04-04T08:24:42Z

Automatic synchronization with BioUML

New page

=== BreakDancer output format (*.ctx) ===

These files produced by BreakDancer software. Each output file is tab-separated text file, which consists of the following columns:

# Chromosome 1
# Position 1
# Orientation 1
# Chromosome 2
# Position 2
# Orientation 2
# Type of a SV
# Size of a SV
# Confidence Score
# Total number of supporting read pairs
# Total number of supporting read pairs from each map file
# Estimated allele frequency
# Software version
# The run parameters

Columns 1-3 and 4-6 are used to specify the coordinates of the two SV breakpoints. The orientation is a string that records the number of reads mapped to the plus (+) or the minus (-) strand in the anchoring regions.

Column 7 is the type of SV detected: DEL (deletions), INS (insertion), INV (inversion), ITX (intra-chromosomal translocation), CTX (inter-chromosomal translocation), and Unknown.

Column 8 is the size of the SV in bp. It is meaningless for inter-chromosomal translocations.

Column 9 is the confidence score associated with the prediction.

Column 11 can be used to dissect the origin of the supporting read pairs, which is useful in pooled analysis. For example, one may want to give SVs that are supported by more than one libraries higher confidence than those detected in only one library. It can also be used to distinguish somatic events from the germline, i.e., those detected in only the tumor libraries versus those detected in both the tumor and the normal libraries.

Column 12 is currently a placeholder for displaying estimated allele frequency. The allele frequencies estimated in this version are not accurate and should not be trusted.

Column 13 and 14 are information useful to reproduce the results.

==== Examples: ====

1 10000 10+0- 2 20000 7+10- CTX -296 99 10 tB<nowiki>|</nowiki>10 1.00 BreakDancerMax-0.0.1 t1

An inter-chromosomal translocation that starts from chr1:10000 and goes into chr2:20000 with 10 supporting read pairs from the library tB and a confidence score of 99.

1 59257 5+1- 1 60164 0+5- DEL 862 99 5 nA<nowiki>|</nowiki>2:tB<nowiki>|</nowiki>1 0.56 BreakDancerMax-0.0.1 c4

A deletion between chr1:59257 and chr1:60164 connected by 5 read pairs, among which 2 in library nA and 1 in library tB support the deletion hypothesis. This deletion is detected by BreakDancerMax-0.0.1 with a separation threshold of 4 s.d.

1 62767 10+0- 1 63126 0+10- INS -13 36 10 NA<nowiki>|</nowiki>10 1.00 BreakDancerMini-0.0.1 q10

An 13 bp insertion detected by BreakDancerMini between chr1:62767 and chr1:63126 with 10 supporting read pairs from a single library <nowiki>'</nowiki>NA<nowiki>'</nowiki> and a confidence score of 36.

==== References ====

# [http://sourceforge.net/projects/breakdancer/ BreakDancer SourceForge page]
# [https://github.com/kenchen/breakdancer BreakDancer readme and format description]

[[Category:File formats]]

@@ Line 2: / Line 2: @@
 :Breakdancer output (*.ctx)
 ;Element type
-:{{Type link|elementType}}
+:{{Type link|track}}
 ;Plugin
 :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

@@ Line 2: / Line 2: @@
 :Breakdancer output (*.ctx)
 ;Element type
-:[[File:Type-track-icon.png]] [[Track (element type)|track]]
+:{{Type link|elementType}}
 ;Plugin
 :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

@@ Line 1: / Line 1: @@
 ;File format title
 :Breakdancer output (*.ctx)
 ;Plugin
 :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

← Older revision		Revision as of 07:12, 7 May 2013
Line 1:		Line 1:
		+	;File format title
		+	:Breakdancer output (*.ctx)
		+	;Plugin
		+	:[[Ru.biosoft.bsa (plugin)\|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
		+
	=== BreakDancer output format (*.ctx) ===		=== BreakDancer output format (*.ctx) ===

← Older revision		Revision as of 09:28, 4 April 2013
Line 52:		Line 52:

	[[Category:File formats]]		[[Category:File formats]]
		+	[[Category:Autogenerated pages]]