.. glossary::
:sorted:
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 :term:`structural variant`.
event type
Classification for a structural variant. see :term:`event_type`.
structural variant
A genomic alteration that can be described by a pair of breakpoints and an :term:`event type`. The two breakpoints represent regions in the genome that are broken apart and reattached together.
breakpoint pair
Basic definition of a :term:`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 :term:`IGV` see
`running IGV with a batch file <https://software.broadinstitute.org/software/igv/batch>`__.
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 :term:`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.
:ref:`HGVS <den-Dunnen-2016>`
Community based standard of reccommendations for variant notation. See http://varnomen.hgvs.org/
BreakDancer
BreakDancer is an SV caller. Source for BreakDancer can be found `here <https://github.com/genome/breakdancer>`__ [Chen-2009]_
BreakSeq
BreakSeq is an SV caller. Source for BreakSeq can be found `here <https://github.com/bioinform/breakseq2>`__ [Abyzov-2015]_
Chimerascan
Chimerascan is an SV caller. Source for Chimerascan can be found `here <https://code.google.com/archive/p/chimerascan>`__ [Iyer-2011]_
CNVnator
CNVnator is an SV caller. Source for CNVnator can be found `here <https://github.com/abyzovlab/CNVnator>`__ [Abyzov-2011]_
DeFuse
DeFuse is an SV caller. Source for DeFuse can be found `here <https://bitbucket.org/dranew/defuse>`__ [McPherson-2011]_
DELLY
DELLY is an SV caller. Source for DELLY can be found `here <https://github.com/dellytools/delly>`__ [Rausch-2012]_
Manta
Manta is an SV caller. Source for Manta can be found `here <https://github.com/Illumina/manta>`__ [Chen-2016]_
STAR-Fusion
STAR-Fusion is an SV caller. Source for STAR-Fusion can be found `here <https://github.com/STAR-Fusion/STAR-Fusion>`__ [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 <https://github.com/Illumina/strelka>`__ [Saunders-2012]_
Pindel
Pindel is an SV caller. Source for Pindel can be found `here <https://github.com/genome/pindel>`__ [Ye-2009]_
Trans-ABySS
Trans-ABySS is an SV caller. Source for Trans-ABySS can be found `here <https://github.com/bcgsc/transabyss>`__ [Robertson-2010]_
SV
Structural Variant
List of column names and their definitions. The types indicated here are the expected types in a row for a given column name.
.. glossary::
:sorted:
library
Identifier for the library/source
cluster_id
Identifier for the merging/clustering step
cluster_size
:class:`int` - The number of breakpoint pair calls that were grouped in creating the cluster
validation_id
Identifier for the validation step
annotation_id
Identifier for the annotation step
product_id
Unique identifier of the final fusion including splicing and ORF decision from the annotation step
event_type
:class:`~mavis.constants.SVTYPE` - The classification of the event
inferred_pairing
A semi colon delimited of event identifiers i.e. <annotation_id>_<splicing pattern>_<cds start>_<cds end>
which were paired to the current event based on predicted products
pairing
A semi colon delimited of event identifiers i.e. <annotation_id>_<splicing pattern>_<cds start>_<cds end>
which were paired to the current event based on breakpoint positions
gene1
Gene for the current annotation at the first breakpoint
gene1_direction
:class:`~mavis.constants.PRIME` - The direction/prime of the gene
gene2
Gene for the current annotation at the second breakpoint
gene2_direction
:class:`~mavis.constants.PRIME` - The direction/prime of the gene. Has the following possible values
gene1_aliases
Other gene names associated with the current annotation at the first breakpoint
gene2_aliases
Other gene names associated with the current annotation at the second breakpoint
gene_product_type
:class:`~mavis.constants.GENE_PRODUCT_TYPE` - Describes if the putative fusion product will be sense or anti-sense
fusion_cdna_coding_end
Position wrt the 5' end of the fusion transcript where coding ends last base of the stop codon
transcript1
Transcript for the current annotation at the first breakpoint
transcript2
Transcript for the current annotation at the second breakpoint
fusion_splicing_pattern
:class:`~mavis.constants.SPLICE_TYPE` - Type of splicing pattern used to create the fusion cDNA.
fusion_cdna_coding_start
:class:`int` - Position wrt the 5' end of the fusion transcript where coding begins first base of the Met amino acid.
fusion_cdna_coding_end
:class:`int` - Position wrt the 5' end of the fusion transcript where coding ends last base of the stop codon
fusion_mapped_domains
``JSON`` - List of domains in :term:`JSON` format where each domain start and end positions are given wrt to the fusion
transcript and the mapping quality is the number of matching amino acid positions over the total
number of amino acids. The sequence is the amino acid sequence of the domain on the reference/original
transcript
fusion_sequence_fasta_id
The sequence identifier for the cdna sequence output fasta file
fusion_sequence_fasta_file
``FILEPATH`` - Path to the corresponding fasta output file
annotation_figure
``FILEPATH`` - File path to the svg drawing representing the annotation
annotation_figure_legend
``JSON`` - :term:`JSON` data for the figure legend
genes_encompassed
Applies to intrachromosomal events only. List of genes which overlap any region that occurs between both
breakpoints. For example in a deletion event these would be deleted genes.
genes_overlapping_break1
list of genes which overlap the first breakpoint
genes_overlapping_break2
list of genes which overlap the second breakpoint
genes_proximal_to_break1
list of genes near the breakpoint and the distance away from the breakpoint
genes_proximal_to_break2
list of genes near the breakpoint and the distance away from the breakpoint
break1_chromosome
:class:`str` - The name of the chromosome on which breakpoint 1 is situated
break1_position_start
:class:`int` - Start integer inclusive 1-based of the range representing breakpoint 1
break1_position_end
:class:`int` - End integer inclusive 1-based of the range representing breakpoint 1
break1_orientation
:class:`~mavis.constants.ORIENT` - The side of the breakpoint wrt the positive/forward strand that is retained.
break1_strand
:class:`~mavis.constants.STRAND` - The strand wrt to the reference positive/forward strand at this breakpoint.
break1_seq
:class:`str` - The sequence up to and including the breakpoint. Always given wrt to the positive/forward strand
break2_chromosome
The name of the chromosome on which breakpoint 2 is situated
break2_position_start
:class:`int` - Start integer inclusive 1-based of the range representing breakpoint 2
break2_position_end
:class:`int` - End integer inclusive 1-based of the range representing breakpoint 2
break2_orientation
:class:`~mavis.constants.ORIENT` - The side of the breakpoint wrt the positive/forward strand that is retained.
break2_strand
:class:`~mavis.constants.STRAND` - The strand wrt to the reference positive/forward strand at this breakpoint.
break2_seq
:class:`str` - The sequence up to and including the breakpoint. Always given wrt to the positive/forward strand
opposing_strands
:class:`bool` - Specifies if breakpoints are on opposite strands wrt to the reference. Expects a boolean
stranded
:class:`bool` - Specifies if the sequencing protocol was strand specific or not. Expects a boolean
protocol
:class:`~mavis.constants.PROTOCOL` - Specifies the type of library
tools
The tools that called the event originally from the cluster step. Should be a semi-colon delimited list of
<tool name>_<tool version>
contigs_assembled
:class:`int` - Number of contigs that were built from split read sequences
contigs_aligned
:class:`int` - Number of contigs that were able to align
contig_alignment_query_name
The query name for the contig alignment. Should match the 'read' name(s) in the .contigs.bam output file
contig_seq
:class:`str` - Sequence of the current contig wrt to the positive forward strand if not strand specific
contig_remap_score
:class:`float` - Score representing the number of sequences from the set of sequences given to the assembly
algorithm that were aligned to the resulting contig with an acceptable scoring based on user-set thresholds.
For any sequence its contribution to the score is divided by the number of mappings to give less weight to
multimaps
call_sequence_complexity
:class:`float` - The minimum amount any two bases account for of the proportion of call sequence. An average for non-contig calls
contig_remapped_reads
:class:`int` - the number of reads from the input bam that map to the assembled contig
contig_remapped_read_names
read query names for the reads that were remapped. A -1 or -2 has been appended to the end of the name to
indicate if this is the first or second read in the pair
contig_alignment_score
:class:`float` - A rank based on the alignment tool blat etc. of the alignment being used. An average if
split alignments were used. Lower numbers indicate a better alignment. If it was the best alignment possible
then this would be zero.
contig_alignment_reference_start
The reference start(s) <chr>:<position> of the contig alignment. Semi-colon delimited
contig_alignment_cigar
The cigar string(s) representing the contig alignment. Semi-colon delimited
contig_remap_coverage
:class:`float` - Fraction of the contig sequence which is covered by the remapped reads
contig_build_score
:class:`int` - Score representing the edge weights of all edges used in building the sequence
contig_strand_specific
:class:`bool` - A flag to indicate if it was possible to resolve the strand for this contig
spanning_reads
:class:`int` - the number of spanning reads which support the event
spanning_read_names
read query names of the spanning reads which support the current event
call_method
:class:`~mavis.constants.CALL_METHOD` - The method used to call the breakpoints
flanking_pairs
:class:`int` - Number of read-pairs where one read aligns to the first breakpoint window and the second read
aligns to the other. The count here is based on the number of unique query names
flanking_pairs_compatible
:class:`int` - Number of flanking pairs of a compatible orientation type. This applies to insertions and
duplications. Flanking pairs supporting an insertion will be compatible to a duplication and flanking pairs
supporting a duplication will be compatible to an insertion (possibly indicating an internal translocation)
flanking_median_fragment_size
:class:`int` - The median fragment size of the flanking reads being used as evidence
flanking_stdev_fragment_size
:class:`float` - The standard deviation in fragment size of the flanking reads being used as evidence
break1_split_reads
:class:`int` - Number of split reads that call the exact breakpoint given
break1_split_reads_forced
:class:`int` - Number of split reads which were aligned to the opposite breakpoint window using a targeted
alignment
break2_split_reads
:class:`int` - Number of split reads that call the exact breakpoint given
break2_split_reads_forced
:class:`int` - Number of split reads which were aligned to the opposite breakpoint window using a targeted
alignment
linking_split_reads
:class:`int` - Number of split reads that align to both breakpoints
untemplated_seq
:class:`str` - The untemplated/novel sequence between the breakpoints
break1_homologous_seq
:class:`str` - Sequence in common at the first breakpoint and other side of the second breakpoint
break2_homologous_seq
:class:`str` - Sequence in common at the second breakpoint and other side of the first breakpoint
break1_ewindow
``int-int`` - Window where evidence was gathered for the first breakpoint
break1_ewindow_count
:class:`int` - Number of reads processed/looked-at in the first evidence window
break1_ewindow_practical_coverage
:class:`float` - break2_ewindow_practical_coverage, break1_ewindow_count / len(break1_ewindow). Not the actual
coverage as bins are sampled within and there is a read limit cutoff
break2_ewindow
``int-int`` - Window where evidence was gathered for the second breakpoint
break2_ewindow_count
:class:`int` - Number of reads processed/looked-at in the second evidence window
break2_ewindow_practical_coverage
:class:`float` - break2_ewindow_practical_coverage, break2_ewindow_count / len(break2_ewindow). Not the actual
coverage as bins are sampled within and there is a read limit cutoff
raw_flanking_pairs
:class:`int` - Number of flanking reads before calling the breakpoint. The count here is based on the number of
unique query names
raw_spanning_reads
:class:`int` - Number of spanning reads collected during evidence collection before calling the breakpoint
raw_break1_split_reads
:class:`int` - Number of split reads before calling the breakpoint
raw_break2_split_reads
:class:`int` - Number of split reads before calling the breakpoint
cdna_synon
semi-colon delimited list of transcript ids which have an identical cdna sequence to the cdna sequence of the
current fusion product
protein_synon
semi-colon delimited list of transcript ids which produce a translation with an identical amino-acid sequence
to the current fusion product
tracking_id
column used to store input identifiers from the original SV calls. Used to track calls from the input files to
the final outputs.
fusion_protein_hgvs
:class:`str` - Describes the fusion protein in HGVS notation. Will be None if the change is not an indel or is synonymous
net_size
``int-int`` - The net size of an event. For translocations and inversion this will always be 0. For indels it will be
negative for deletions and positive for insertions. It is a range to accommodate non-specific events.
supplementary_call
:class:`bool` - Flag to indicate if the current event was a supplementary call, meaning a call that was found as a result of
validating another event.