Glossary
flanking read pair
A pair of reads where one read maps to one side of a set of breakpoints and its mate maps to the other.
split read
A read which aligns next to a breakpoint and is softclipped at one or more sides.
spanning read
Applies primarily to small structural variants. Reads which span both breakpoints.
half-mapped read
A read whose mate is unaligned. Generally this refers to reads in the evidence stage that are mapped next to a breakpoint.
breakpoint
A breakpoint is a genomic position (interval) on some reference/template/chromosome which has a strand and orientation. The orientation describes the portion of the reference that is retained.
event
Used interchangeably with structural variant.
event type
Classification for a structural variant. see event_type.
structural variant
A genomic alteration that can be described by a pair of breakpoints and an event type. The two breakpoints represent regions in the genome that are broken apart and reattached together.
breakpoint pair
Basic definition of a structural variant. Does not automatically imply a classification/type.
bed
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format1.
IGV batch file
This is a file format type defined by IGV see running IGV with a batch file.
BAM
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format5.1.
2bit
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format7.
fasta
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format18.
psl
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format2.
pslx
Extended format of a psl.
SVG
SVG (Scalable vector graph) is an image format. see https://www.w3schools.com/graphics/svg_intro.asp.
JSON
JSON (JavaScript Object Notation) is a data file format. see https://www.w3schools.com/js/js_json_intro.asp.
blat
Alignment tool. see https://genome.ucsc.edu/FAQ/FAQblat.html#blat3 for instructions on download and install.
IGV
Integrative Genomics Viewer is a visualization tool. see http://software.broadinstitute.org/software/igv.
SGE
Sun Grid Engine (SGE) is a job scheduling system for cluster management see http://star.mit.edu/cluster/docs/0.93.3/guides/sge.html.
SLURM
SLURM is a job scheduling system for cluster management see https://slurm.schedmd.com/archive/slurm-17.02.1.
TORQUE
TORQUE is a job scheduling system for cluster management see http://www.adaptivecomputing.com/products/open-source/torque/.
BWA
BWA is an alignement tool. See https://github.com/lh3/bwa for install instructions.
HGVS
Community based standard of reccommendations for variant notation. See http://varnomen.hgvs.org/
Arriba
Arriba is an SV caller. Source for Arriba can be found here Uhrig-2021
BreakDancer
BreakDancer is an SV caller. Source for BreakDancer can be found here Chen-2009
BreakSeq
BreakSeq is an SV caller. Source for BreakSeq can be found here Abyzov-2015
Chimerascan
Chimerascan is an SV caller. Source for Chimerascan can be found here Iyer-2011
CNVnator
CNVnator is an SV caller. Source for CNVnator can be found here Abyzov-2011
DeFuse
DeFuse is an SV caller. Source for DeFuse can be found here McPherson-2011
DELLY
DELLY is an SV caller. Source for DELLY can be found here Rausch-2012
Manta
Manta is an SV caller. Source for Manta can be found here Chen-2016
STAR-Fusion
STAR-Fusion is an SV caller. Source for STAR-Fusion can be found here Haas-2017
Strelka
Strelka is an SNV and small indel caller. Only the small indels can be processed, since SNVs are not currently suported. Source for Strelka can be found here Saunders-2012
Pindel
Pindel is an SV caller. Source for Pindel can be found here Ye-2009
Trans-ABySS
Trans-ABySS is an SV caller. Source for Trans-ABySS can be found here Robertson-2010
SV
Structural Variant