Glossary

General Terms

2bit
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format7.
bam
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format5.1.
bed
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format1.
blat
Alignment tool. see https://genome.ucsc.edu/FAQ/FAQblat.html.
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.
breakpoint pair
Basic definition of a structural variant. Does not automatically imply a classification/type.
BWA
BWA is an alignement tool. See https://github.com/lh3/bwa
event
Used interchangeably with structural variant.
event type
Classification for a structural variant. see event_type.
fasta
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format18.
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.
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.
HGVS
Community based standard of reccommendations for variant notation. See http://varnomen.hgvs.org/
IGV
Integrative Genomics Viewer is a visualization tool. see http://software.broadinstitute.org/software/igv.
IGV batch file
This is a file format type defined by IGV see running IGV with a batch file.
JSON
JSON (JavaScript Object Notation) is a data file format. see https://www.w3schools.com/js/js_json_intro.asp.
psl
File format specification. See https://genome.ucsc.edu/FAQ/FAQformat#format2.
pslx
Extended format of a psl.
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/quickstart.html.
spanning read
Applies primarily to small structural variants. Reads which span both breakpoints.
split read
A read which aligns next to a breakpoint and is softclipped at one or more sides.
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.
SVG
SVG (Scalable vector graph) is an image format. see https://www.w3schools.com/graphics/svg_intro.asp.

Configurable Settings

aligner
SUPPORTED_ALIGNER - The aligner to use to map the contigs/reads back to the reference e.g blat or bwa. The corresponding environment variable is MAVIS_ALIGNER and the default value is 'blat'. Accepted values include: 'bwa mem', 'blat'
annotation_filters
str - A comma separated list of filters to apply to putative annotations. The corresponding environment variable is MAVIS_ANNOTATION_FILTERS and the default value is 'choose_more_annotated,choose_transcripts_by_priority'
annotation_memory
int - Default memory limit (mb) for the annotation stage. The corresponding environment variable is MAVIS_ANNOTATION_MEMORY and the default value is 12000
assembly_include_flanking_pairs
bool - If true then when the split reads are assembled, any flanking read pairs will also be added. The corresponding environment variable is MAVIS_ASSEMBLY_INCLUDE_FLANKING_PAIRS and the default value is True
assembly_include_half_mapped_reads
bool - If true then when the split reads are assembled, any half-mapped read mates will also be added. The corresponding environment variable is MAVIS_ASSEMBLY_INCLUDE_HALF_MAPPED_READS and the default value is True
assembly_max_kmer_size
int - The minimum between this and the smallest length input sequence is used as the kmer size for assembling the debruijn graph. if this is not set (any value less than 0 is considered not set) the default is the 75%% of the minimum length input sequence. The corresponding environment variable is MAVIS_ASSEMBLY_MAX_KMER_SIZE and the default value is -1
assembly_max_kmer_strict
bool - If true then any sequences input to the assembly algorithm that cannot create a kmer of this size will be discarded. if false, then the kmer size will be reduced to the minimum input and all input sequences will be used in the assembly algorithm. The corresponding environment variable is MAVIS_ASSEMBLY_MAX_KMER_STRICT and the default value is True
assembly_max_paths
int - The maximum number of paths to resolve. this is used to limit when there is a messy assembly graph to resolve. the assembly will pre-calculate the number of paths (or putative assemblies) and stop if it is greater than the given setting. The corresponding environment variable is MAVIS_ASSEMBLY_MAX_PATHS and the default value is 4
assembly_min_edge_weight
int - Discards all edges with a weight/frequency less than this from the debruijn graph. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_EDGE_WEIGHT and the default value is 2
assembly_min_exact_match_to_remap
int - The minimum length of exact matches to initiate remapping a read to a contig. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_EXACT_MATCH_TO_REMAP and the default value is 15
assembly_min_nc_edge_weight
int - Discards all non-cutting edges with a weight/frequency less than this from the debruijn graph. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_NC_EDGE_WEIGHT and the default value is 4
assembly_min_remap_coverage
float_fraction - Minimum fraction of the contig sequence which the remapped sequences must align over. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_REMAP_COVERAGE and the default value is 0.9
assembly_min_remapped_seq
int - The minimum input sequences that must remap for an assembled contig to be used. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_REMAPPED_SEQ and the default value is 3
assembly_min_tgt_to_exclude_half_map
int - The minimum number of split reads aligning to both breakpoints in order to exclude half-mapped reads from the assembly input. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_TGT_TO_EXCLUDE_HALF_MAP and the default value is 7
assembly_min_uniq
float_fraction - Minimum percent uniq required to keep separate assembled contigs. if contigs are more similar then the lower scoring contig is dropped. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_UNIQ and the default value is 0.01
assembly_strand_concordance
float_fraction - When the number of remapped reads from each strand are compared, the ratio must be above this number to decide on the strand. The corresponding environment variable is MAVIS_ASSEMBLY_STRAND_CONCORDANCE and the default value is 0.51
blat_limit_top_aln
int - Number of results to return from blat (ranking based on score). The corresponding environment variable is MAVIS_BLAT_LIMIT_TOP_ALN and the default value is 10
blat_min_identity
float_fraction - The minimum percent identity match required for blat results when aligning contigs. The corresponding environment variable is MAVIS_BLAT_MIN_IDENTITY and the default value is 0.9
breakpoint_color
str - Breakpoint outline color. The corresponding environment variable is MAVIS_BREAKPOINT_COLOR and the default value is '#000000'
call_error
int - Buffer zone for the evidence window. The corresponding environment variable is MAVIS_CALL_ERROR and the default value is 10
cluster_initial_size_limit
int - The maximum cumulative size of both breakpoints for breakpoint pairs to be used in the initial clustering phase (combining based on overlap). The corresponding environment variable is MAVIS_CLUSTER_INITIAL_SIZE_LIMIT and the default value is 25
cluster_radius
int - Maximum distance allowed between paired breakpoint pairs. The corresponding environment variable is MAVIS_CLUSTER_RADIUS and the default value is 100
contig_aln_max_event_size
int - Relates to determining breakpoints when pairing contig alignments. for any given read in a putative pair the soft clipping is extended to include any events of greater than this size. the softclipping is added to the side of the alignment as indicated by the breakpoint we are assigning pairs to. The corresponding environment variable is MAVIS_CONTIG_ALN_MAX_EVENT_SIZE and the default value is 50
contig_aln_merge_inner_anchor
int - The minimum number of consecutive exact match base pairs to not merge events within a contig alignment. The corresponding environment variable is MAVIS_CONTIG_ALN_MERGE_INNER_ANCHOR and the default value is 20
contig_aln_merge_outer_anchor
int - Minimum consecutively aligned exact matches to anchor an end for merging internal events. The corresponding environment variable is MAVIS_CONTIG_ALN_MERGE_OUTER_ANCHOR and the default value is 15
contig_aln_min_anchor_size
int - The minimum number of aligned bases for a contig (m or =) in order to simplify. do not have to be consecutive. The corresponding environment variable is MAVIS_CONTIG_ALN_MIN_ANCHOR_SIZE and the default value is 50
contig_aln_min_extend_overlap
int - Minimum number of bases the query coverage interval must be extended by in order to pair alignments as a single split alignment. The corresponding environment variable is MAVIS_CONTIG_ALN_MIN_EXTEND_OVERLAP and the default value is 10
contig_aln_min_query_consumption
float_fraction - Minimum fraction of the original query sequence that must be used by the read(s) of the alignment. The corresponding environment variable is MAVIS_CONTIG_ALN_MIN_QUERY_CONSUMPTION and the default value is 0.9
contig_aln_min_score
float_fraction - Minimum score for a contig to be used as evidence in a call by contig. The corresponding environment variable is MAVIS_CONTIG_ALN_MIN_SCORE and the default value is 0.9
contig_call_distance
int - The maximum distance allowed between breakpoint pairs (called by contig) in order for them to pair. The corresponding environment variable is MAVIS_CONTIG_CALL_DISTANCE and the default value is 0
domain_color
str - Domain fill color. The corresponding environment variable is MAVIS_DOMAIN_COLOR and the default value is '#ccccb3'
domain_mismatch_color
str - Domain fill color on 0%% match. The corresponding environment variable is MAVIS_DOMAIN_MISMATCH_COLOR and the default value is '#b2182b'
domain_name_regex_filter
str - The regular expression used to select domains to be displayed (filtered by name). The corresponding environment variable is MAVIS_DOMAIN_NAME_REGEX_FILTER and the default value is '^PF\\d+$'
domain_scaffold_color
str - The color of the domain scaffold. The corresponding environment variable is MAVIS_DOMAIN_SCAFFOLD_COLOR and the default value is '#000000'
draw_fusions_only
bool - Flag to indicate if events which do not produce a fusion transcript should produce illustrations. The corresponding environment variable is MAVIS_DRAW_FUSIONS_ONLY and the default value is True
draw_non_synonymous_cdna_only
bool - Flag to indicate if events which are synonymous at the cdna level should produce illustrations. The corresponding environment variable is MAVIS_DRAW_NON_SYNONYMOUS_CDNA_ONLY and the default value is True
drawing_width_iter_increase
int - The amount (in pixels) by which to increase the drawing width upon failure to fit. The corresponding environment variable is MAVIS_DRAWING_WIDTH_ITER_INCREASE and the default value is 500
fetch_min_bin_size
int - The minimum size of any bin for reading from a bam file. increasing this number will result in smaller bins being merged or less bins being created (depending on the fetch method). The corresponding environment variable is MAVIS_FETCH_MIN_BIN_SIZE and the default value is 50
fetch_reads_bins
int - Number of bins to split an evidence window into to ensure more even sampling of high coverage regions. The corresponding environment variable is MAVIS_FETCH_READS_BINS and the default value is 5
fetch_reads_limit
int - Maximum number of reads, cap, to loop over for any given evidence window. The corresponding environment variable is MAVIS_FETCH_READS_LIMIT and the default value is 3000
filter_cdna_synon
bool - Filter all annotations synonymous at the cdna level. The corresponding environment variable is MAVIS_FILTER_CDNA_SYNON and the default value is True
filter_min_flanking_reads
int - Minimum number of flanking pairs for a call by flanking pairs. The corresponding environment variable is MAVIS_FILTER_MIN_FLANKING_READS and the default value is 10
filter_min_linking_split_reads
int - Minimum number of linking split reads for a call by split reads. The corresponding environment variable is MAVIS_FILTER_MIN_LINKING_SPLIT_READS and the default value is 1
filter_min_remapped_reads
int - Minimum number of remapped reads for a call by contig. The corresponding environment variable is MAVIS_FILTER_MIN_REMAPPED_READS and the default value is 5
filter_min_spanning_reads
int - Minimum number of spanning reads for a call by spanning reads. The corresponding environment variable is MAVIS_FILTER_MIN_SPANNING_READS and the default value is 5
filter_min_split_reads
int - Minimum number of split reads for a call by split reads. The corresponding environment variable is MAVIS_FILTER_MIN_SPLIT_READS and the default value is 5
filter_protein_synon
bool - Filter all annotations synonymous at the protein level. The corresponding environment variable is MAVIS_FILTER_PROTEIN_SYNON and the default value is True
filter_secondary_alignments
bool - Filter secondary alignments when gathering read evidence. The corresponding environment variable is MAVIS_FILTER_SECONDARY_ALIGNMENTS and the default value is True
flanking_call_distance
int - The maximum distance allowed between breakpoint pairs (called by flanking pairs) in order for them to pair. The corresponding environment variable is MAVIS_FLANKING_CALL_DISTANCE and the default value is 0
fuzzy_mismatch_number
int - The number of events/mismatches allowed to be considered a fuzzy match. The corresponding environment variable is MAVIS_FUZZY_MISMATCH_NUMBER and the default value is 1
gene1_color
str - The color of genes near the first gene. The corresponding environment variable is MAVIS_GENE1_COLOR and the default value is '#657e91'
gene1_color_selected
str - The color of the first gene. The corresponding environment variable is MAVIS_GENE1_COLOR_SELECTED and the default value is '#518dc5'
gene2_color
str - The color of genes near the second gene. The corresponding environment variable is MAVIS_GENE2_COLOR and the default value is '#325556'
gene2_color_selected
str - The color of the second gene. The corresponding environment variable is MAVIS_GENE2_COLOR_SELECTED and the default value is '#4c9677'
import_env
bool - Flag to import environment variables. The corresponding environment variable is MAVIS_IMPORT_ENV and the default value is True
input_call_distance
int - The maximum distance allowed between breakpoint pairs (called by input tools, not validated) in order for them to pair. The corresponding environment variable is MAVIS_INPUT_CALL_DISTANCE and the default value is 5
label_color
str - The label color. The corresponding environment variable is MAVIS_LABEL_COLOR and the default value is '#000000'
limit_to_chr
ChrListString - A semi-colon delimited list of chromosome names to use. breakpointpairs on other chromosomes will be filteredout. for example ‘1;2;3;4’ would filter out events/breakpoint pairs on any chromosomes but 1, 2, 3, and 4. The corresponding environment variable is MAVIS_LIMIT_TO_CHR and the default value is ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y']
mask_fill
str - Color of mask (for deleted region etc.). The corresponding environment variable is MAVIS_MASK_FILL and the default value is '#ffffff'
mask_opacity
float_fraction - Opacity of the mask layer. The corresponding environment variable is MAVIS_MASK_OPACITY and the default value is 0.7
max_drawing_retries
int - The maximum number of retries for attempting a drawing. each iteration the width is extended. if it is still insufficient after this number a gene-level only drawing will be output. The corresponding environment variable is MAVIS_MAX_DRAWING_RETRIES and the default value is 3
max_files
int - The maximum number of files to output from clustering/splitting. The corresponding environment variable is MAVIS_MAX_FILES and the default value is 200
max_orf_cap
int - The maximum number of orfs to return (best putative orfs will be retained). The corresponding environment variable is MAVIS_MAX_ORF_CAP and the default value is 3
max_proximity
int - The maximum distance away from an annotation before the region in considered to be uninformative. The corresponding environment variable is MAVIS_MAX_PROXIMITY and the default value is 5000
max_sc_preceeding_anchor
int - When remapping a softclipped read this determines the amount of softclipping allowed on the side opposite of where we expect it. for example for a softclipped read on a breakpoint with a left orientation this limits the amount of softclipping that is allowed on the right. if this is set to none then there is no limit on softclipping. The corresponding environment variable is MAVIS_MAX_SC_PRECEEDING_ANCHOR and the default value is 6
memory_limit
int - The maximum number of megabytes (mb) any given job is allowed. The corresponding environment variable is MAVIS_MEMORY_LIMIT and the default value is 16000
min_anchor_exact
int - Applies to re-aligning softclipped reads to the opposing breakpoint. the minimum number of consecutive exact matches to anchor a read to initiate targetted realignment. The corresponding environment variable is MAVIS_MIN_ANCHOR_EXACT and the default value is 6
min_anchor_fuzzy
int - Applies to re-aligning softclipped reads to the opposing breakpoint. the minimum length of a fuzzy match to anchor a read to initiate targetted realignment. The corresponding environment variable is MAVIS_MIN_ANCHOR_FUZZY and the default value is 10
min_anchor_match
float_fraction - Minimum percent match for a read to be kept as evidence. The corresponding environment variable is MAVIS_MIN_ANCHOR_MATCH and the default value is 0.9
min_clusters_per_file
int - The minimum number of breakpoint pairs to output to a file. The corresponding environment variable is MAVIS_MIN_CLUSTERS_PER_FILE and the default value is 50
min_domain_mapping_match
float_fraction - A number between 0 and 1 representing the minimum percent match a domain must map to the fusion transcript to be displayed. The corresponding environment variable is MAVIS_MIN_DOMAIN_MAPPING_MATCH and the default value is 0.9
min_double_aligned_to_estimate_insertion_size
int - The minimum number of reads which map soft-clipped to both breakpoints to assume the size of the untemplated sequence between the breakpoints is at most the read length - 2 * min_softclipping. The corresponding environment variable is MAVIS_MIN_DOUBLE_ALIGNED_TO_ESTIMATE_INSERTION_SIZE and the default value is 2
min_flanking_pairs_resolution
int - The minimum number of flanking reads required to call a breakpoint by flanking evidence. The corresponding environment variable is MAVIS_MIN_FLANKING_PAIRS_RESOLUTION and the default value is 10
min_linking_split_reads
int - The minimum number of split reads which aligned to both breakpoints. The corresponding environment variable is MAVIS_MIN_LINKING_SPLIT_READS and the default value is 2
min_mapping_quality
int - The minimum mapping quality of reads to be used as evidence. The corresponding environment variable is MAVIS_MIN_MAPPING_QUALITY and the default value is 5
min_non_target_aligned_split_reads
int - The minimum number of split reads aligned to a breakpoint by the input bam and no forced by local alignment to the target region to call a breakpoint by split read evidence. The corresponding environment variable is MAVIS_MIN_NON_TARGET_ALIGNED_SPLIT_READS and the default value is 1
min_orf_size
int - The minimum length (in amino acids) to retain a putative open reading frame (orf). The corresponding environment variable is MAVIS_MIN_ORF_SIZE and the default value is 300
min_sample_size_to_apply_percentage
int - Minimum number of aligned bases to compute a match percent. if there are less than this number of aligned bases (match or mismatch) the percent comparator is not used. The corresponding environment variable is MAVIS_MIN_SAMPLE_SIZE_TO_APPLY_PERCENTAGE and the default value is 10
min_softclipping
int - Minimum number of soft-clipped bases required for a read to be used as soft-clipped evidence. The corresponding environment variable is MAVIS_MIN_SOFTCLIPPING and the default value is 6
min_spanning_reads_resolution
int - Minimum number of spanning reads required to call an event by spanning evidence. The corresponding environment variable is MAVIS_MIN_SPANNING_READS_RESOLUTION and the default value is 5
min_splits_reads_resolution
int - Minimum number of split reads required to call a breakpoint by split reads. The corresponding environment variable is MAVIS_MIN_SPLITS_READS_RESOLUTION and the default value is 3
novel_exon_color
str - Novel exon fill color. The corresponding environment variable is MAVIS_NOVEL_EXON_COLOR and the default value is '#000000'
outer_window_min_event_size
int - The minimum size of an event in order for flanking read evidence to be collected. The corresponding environment variable is MAVIS_OUTER_WINDOW_MIN_EVENT_SIZE and the default value is 125
queue
str - The queue jobs are to be submitted to. The corresponding environment variable is MAVIS_QUEUE and the default value is ''
scaffold_color
str - The color used for the gene/transcripts scaffolds. The corresponding environment variable is MAVIS_SCAFFOLD_COLOR and the default value is '#000000'
scheduler
SCHEDULER - The scheduler being used. The corresponding environment variable is MAVIS_SCHEDULER and the default value is 'SLURM'. Accepted values include: 'SGE', 'SLURM'
spanning_call_distance
int - The maximum distance allowed between breakpoint pairs (called by spanning reads) in order for them to pair. The corresponding environment variable is MAVIS_SPANNING_CALL_DISTANCE and the default value is 5
splice_color
str - Splicing lines color. The corresponding environment variable is MAVIS_SPLICE_COLOR and the default value is '#000000'
split_call_distance
int - The maximum distance allowed between breakpoint pairs (called by split reads) in order for them to pair. The corresponding environment variable is MAVIS_SPLIT_CALL_DISTANCE and the default value is 10
stdev_count_abnormal
float - The number of standard deviations away from the normal considered expected and therefore not qualifying as flanking reads. The corresponding environment variable is MAVIS_STDEV_COUNT_ABNORMAL and the default value is 3.0
strand_determining_read
int - 1 or 2. the read in the pair which determines if (assuming a stranded protocol) the first or second read in the pair matches the strand sequenced. The corresponding environment variable is MAVIS_STRAND_DETERMINING_READ and the default value is 2
time_limit
int - The time in seconds any given jobs is allowed. The corresponding environment variable is MAVIS_TIME_LIMIT and the default value is 57600
trans_validation_memory
int - Default memory limit (mb) for the validation stage (for transcriptomes). The corresponding environment variable is MAVIS_TRANS_VALIDATION_MEMORY and the default value is 18000
uninformative_filter
bool - Flag that determines if breakpoint pairs which are not within max_proximity to any annotations are filtered out prior to clustering. The corresponding environment variable is MAVIS_UNINFORMATIVE_FILTER and the default value is True
validation_memory
int - Default memory limit (mb) for the validation stage. The corresponding environment variable is MAVIS_VALIDATION_MEMORY and the default value is 16000
width
int - The drawing width in pixels. The corresponding environment variable is MAVIS_WIDTH and the default value is 1000

Column Names

List of column names and their definitions. The types indicated here are the expected types in a row for a given column name.

annotation_figure
FILEPATH - File path to the svg drawing representing the annotation
annotation_figure_legend
JSON - JSON data for the figure legend
annotation_id
Identifier for the annotation step
break1_chromosome
str - The name of the chromosome on which breakpoint 1 is situated
break1_ewindow
int-int - Window where evidence was gathered for the first breakpoint
break1_ewindow_count
int - Number of reads processed/looked-at in the first evidence window
break1_ewindow_practical_coverage
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
break1_homologous_seq
str - Sequence in common at the first breakpoint and other side of the second breakpoint
break1_orientation
ORIENT - The side of the breakpoint wrt the positive/forward strand that is retained.
break1_position_end
int - End integer inclusive 1-based of the range representing breakpoint 1
break1_position_start
int - Start integer inclusive 1-based of the range representing breakpoint 1
break1_seq
str - The sequence up to and including the breakpoint. Always given wrt to the positive/forward strand
break1_split_reads
int - Number of split reads that call the exact breakpoint given
break1_split_reads_forced
int - Number of split reads which were aligned to the opposite breakpoint window using a targeted alignment
break1_strand
STRAND - The strand wrt to the reference positive/forward strand at this breakpoint.
break2_chromosome
The name of the chromosome on which breakpoint 2 is situated
break2_ewindow
int-int - Window where evidence was gathered for the second breakpoint
break2_ewindow_count
int - Number of reads processed/looked-at in the second evidence window
break2_ewindow_practical_coverage
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
break2_homologous_seq
str - Sequence in common at the second breakpoint and other side of the first breakpoint
break2_orientation
ORIENT - The side of the breakpoint wrt the positive/forward strand that is retained.
break2_position_end
int - End integer inclusive 1-based of the range representing breakpoint 2
break2_position_start
int - Start integer inclusive 1-based of the range representing breakpoint 2
break2_seq
str - The sequence up to and including the breakpoint. Always given wrt to the positive/forward strand
break2_split_reads
int - Number of split reads that call the exact breakpoint given
break2_split_reads_forced
int - Number of split reads which were aligned to the opposite breakpoint window using a targeted alignment
break2_strand
STRAND - The strand wrt to the reference positive/forward strand at this breakpoint.
call_method
CALL_METHOD - The method used to call the breakpoints
cdna_synon
semi-colon delimited list of transcript ids which have an identical cdna sequence to the cdna sequence of the current fusion product
cluster_id
Identifier for the merging/clustering step
cluster_size
int - The number of breakpoint pair calls that were grouped in creating the cluster
contig_alignment_cigar
The cigar string(s) representing the contig alignment. Semi-colon delimited
contig_alignment_query_name
The query name for the contig alignment. Should match the ‘read’ name(s) in the .contigs.bam output file
contig_alignment_reference_start
The reference start(s) <chr>:<position> of the contig alignment. Semi-colon delimited
contig_alignment_score
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_build_score
int - Score representing the edge weights of all edges used in building the sequence
contig_remap_coverage
float - Fraction of the contig sequence which is covered by the remapped reads
contig_remap_score
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
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_remapped_reads
int - the number of reads from the input bam that map to the assembled contig
contig_seq
str - Sequence of the current contig wrt to the positive forward strand if not strand specific
contig_strand_specific
bool - A flag to indicate if it was possible to resolve the strand for this contig
contigs_aligned
int - Number of contigs that were able to align
contigs_assembled
int - Number of contigs that were built from split read sequences
event_type
SVTYPE - The classification of the event
flanking_median_fragment_size
int - The median fragment size of the flanking reads being used as evidence
flanking_pairs
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
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_stdev_fragment_size
float - The standard deviation in fragment size of the flanking reads being used as evidence
fusion_cdna_coding_end
Position wrt the 5’ end of the fusion transcript where coding ends last base of the stop codon
fusion_cdna_coding_end
int - Position wrt the 5’ end of the fusion transcript where coding ends last base of the stop codon
fusion_cdna_coding_start
int - Position wrt the 5’ end of the fusion transcript where coding begins first base of the Met amino acid.
fusion_mapped_domains
JSON - List of domains in 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_protein_hgvs
str - Describes the fusion protein in HGVS notation. Will be None if the change is not an indel or is synonymous
fusion_sequence_fasta_file
FILEPATH - Path to the corresponding fasta output file
fusion_sequence_fasta_id
The sequence identifier for the cdna sequence output fasta file
fusion_splicing_pattern
SPLICE_TYPE - Type of splicing pattern used to create the fusion cDNA.
gene1
Gene for the current annotation at the first breakpoint
gene1_aliases
Other gene names associated with the current annotation at the first breakpoint
gene1_direction
PRIME - The direction/prime of the gene
gene2
Gene for the current annotation at the second breakpoint
gene2_aliases
Other gene names associated with the current annotation at the second breakpoint
gene2_direction
PRIME - The direction/prime of the gene. Has the following possible values
gene_product_type
GENE_PRODUCT_TYPE - Describes if the putative fusion product will be sense or anti-sense
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
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
library
Identifier for the library/source
linking_split_reads
int - Number of split reads that align to both breakpoints
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.
opposing_strands
bool - Specifies if breakpoints are on opposite strands wrt to the reference. Expects a boolean
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
product_id
Unique identifier of the final fusion including splicing and ORF decision from the annotation step
protein_synon
semi-colon delimited list of transcript ids which produce a translation with an identical amino-acid sequence to the current fusion product
protocol
PROTOCOL - Specifies the type of library
raw_break1_split_reads
int - Number of split reads before calling the breakpoint
raw_break2_split_reads
int - Number of split reads before calling the breakpoint
raw_flanking_pairs
int - Number of flanking reads before calling the breakpoint. The count here is based on the number of unique query names
raw_spanning_reads
int - Number of spanning reads collected during evidence collection before calling the breakpoint
spanning_read_names
read query names of the spanning reads which support the current event
spanning_reads
int - the number of spanning reads which support the event
stranded
bool - Specifies if the sequencing protocol was strand specific or not. Expects a boolean
tools
The tools that called the event originally from the cluster step. Should be a semi-colon delimited list of <tool name>_<tool version>
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.
transcript1
Transcript for the current annotation at the first breakpoint
transcript2
Transcript for the current annotation at the second breakpoint
untemplated_seq
str - The untemplated/novel sequence between the breakpoints
validation_id
Identifier for the validation step