Configurable Settings
aligner
type: mavis.align.SUPPORTED_ALIGNER
environment variable: MAVIS_ALIGNER
default: 'blat'
accepted values: 'bwa mem', 'blat'
The aligner to use to map the contigs/reads back to the reference e.g blat or bwa
aligner_reference
type: filepath
environment variable: MAVIS_ALIGNER_REFERENCE
default: None
Path to the aligner reference file used for aligning the contig sequences
annotation_filters
type: str
environment variable: MAVIS_ANNOTATION_FILTERS
default: 'choose_more_annotated,choose_transcripts_by_priority'
A comma separated list of filters to apply to putative annotations
annotation_memory
type: int
environment variable: MAVIS_ANNOTATION_MEMORY
default: 12000
Default memory limit (mb) for the annotation stage
annotations
type: filepath
environment variable: MAVIS_ANNOTATIONS
default: []
Path to the reference annotations of genes, transcript, exons, domains, etc
assembly_kmer_size
type: float_fraction
environment variable: MAVIS_ASSEMBLY_KMER_SIZE
default: 0.74
The percent of the read length to make kmers for assembly
assembly_max_paths
type: int
environment variable: MAVIS_ASSEMBLY_MAX_PATHS
default: 8
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
assembly_min_edge_trim_weight
type: int
environment variable: MAVIS_ASSEMBLY_MIN_EDGE_TRIM_WEIGHT
default: 3
This is used to simplify the debruijn graph before path finding. edges with less than this frequency will be discarded if they are non-cutting, at a fork, or the end of a path
assembly_min_exact_match_to_remap
type: int
environment variable: MAVIS_ASSEMBLY_MIN_EXACT_MATCH_TO_REMAP
default: 15
The minimum length of exact matches to initiate remapping a read to a contig
assembly_min_remap_coverage
type: float_fraction
environment variable: MAVIS_ASSEMBLY_MIN_REMAP_COVERAGE
default: 0.9
Minimum fraction of the contig sequence which the remapped sequences must align over
assembly_min_remapped_seq
type: int
environment variable: MAVIS_ASSEMBLY_MIN_REMAPPED_SEQ
default: 3
The minimum input sequences that must remap for an assembled contig to be used
assembly_min_uniq
type: float_fraction
environment variable: MAVIS_ASSEMBLY_MIN_UNIQ
default: 0.1
Minimum percent uniq required to keep separate assembled contigs. if contigs are more similar then the lower scoring, then shorter, contig is dropped
assembly_strand_concordance
type: float_fraction
environment variable: MAVIS_ASSEMBLY_STRAND_CONCORDANCE
default: 0.51
When the number of remapped reads from each strand are compared, the ratio must be above this number to decide on the strand
blat_limit_top_aln
type: int
environment variable: MAVIS_BLAT_LIMIT_TOP_ALN
default: 10
Number of results to return from blat (ranking based on score)
blat_min_identity
type: float_fraction
environment variable: MAVIS_BLAT_MIN_IDENTITY
default: 0.9
The minimum percent identity match required for blat results when aligning contigs
breakpoint_color
type: str
environment variable: MAVIS_BREAKPOINT_COLOR
default: '#000000'
Breakpoint outline color
call_error
type: int
environment variable: MAVIS_CALL_ERROR
default: 10
Buffer zone for the evidence window
clean_aligner_files
type: cast_boolean
environment variable: MAVIS_CLEAN_ALIGNER_FILES
default: False
Remove the aligner output files after the validation stage is complete. not required for subsequent steps but can be useful in debugging and deep investigation of events
cluster_initial_size_limit
type: int
environment variable: MAVIS_CLUSTER_INITIAL_SIZE_LIMIT
default: 25
The maximum cumulative size of both breakpoints for breakpoint pairs to be used in the initial clustering phase (combining based on overlap)
cluster_radius
type: int
environment variable: MAVIS_CLUSTER_RADIUS
default: 100
Maximum distance allowed between paired breakpoint pairs
concurrency_limit
type: int
environment variable: MAVIS_CONCURRENCY_LIMIT
default: None
The concurrency limit for tasks in any given job array or the number of concurrent processes allowed for a local run
contig_aln_max_event_size
type: int
environment variable: MAVIS_CONTIG_ALN_MAX_EVENT_SIZE
default: 50
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
contig_aln_merge_inner_anchor
type: int
environment variable: MAVIS_CONTIG_ALN_MERGE_INNER_ANCHOR
default: 20
The minimum number of consecutive exact match base pairs to not merge events within a contig alignment
contig_aln_merge_outer_anchor
type: int
environment variable: MAVIS_CONTIG_ALN_MERGE_OUTER_ANCHOR
default: 15
Minimum consecutively aligned exact matches to anchor an end for merging internal events
contig_aln_min_anchor_size
type: int
environment variable: MAVIS_CONTIG_ALN_MIN_ANCHOR_SIZE
default: 50
The minimum number of aligned bases for a contig (m or =) in order to simplify. do not have to be consecutive
contig_aln_min_extend_overlap
type: int
environment variable: MAVIS_CONTIG_ALN_MIN_EXTEND_OVERLAP
default: 10
Minimum number of bases the query coverage interval must be extended by in order to pair alignments as a single split alignment
contig_aln_min_query_consumption
type: float_fraction
environment variable: MAVIS_CONTIG_ALN_MIN_QUERY_CONSUMPTION
default: 0.9
Minimum fraction of the original query sequence that must be used by the read(s) of the alignment
contig_aln_min_score
type: float_fraction
environment variable: MAVIS_CONTIG_ALN_MIN_SCORE
default: 0.9
Minimum score for a contig to be used as evidence in a call by contig
contig_call_distance
type: int
environment variable: MAVIS_CONTIG_CALL_DISTANCE
default: 10
The maximum distance allowed between breakpoint pairs (called by contig) in order for them to pair
dgv_annotation
type: filepath
environment variable: MAVIS_DGV_ANNOTATION
default: []
Path to the dgv reference processed to look like the cytoband file
domain_color
type: str
environment variable: MAVIS_DOMAIN_COLOR
default: '#ccccb3'
Domain fill color
domain_mismatch_color
type: str
environment variable: MAVIS_DOMAIN_MISMATCH_COLOR
default: '#b2182b'
Domain fill color on 0%% match
domain_name_regex_filter
type: str
environment variable: MAVIS_DOMAIN_NAME_REGEX_FILTER
default: '^PF\\d+$'
The regular expression used to select domains to be displayed (filtered by name)
domain_scaffold_color
type: str
environment variable: MAVIS_DOMAIN_SCAFFOLD_COLOR
default: '#000000'
The color of the domain scaffold
draw_fusions_only
type: cast_boolean
environment variable: MAVIS_DRAW_FUSIONS_ONLY
default: True
Flag to indicate if events which do not produce a fusion transcript should produce illustrations
draw_non_synonymous_cdna_only
type: cast_boolean
environment variable: MAVIS_DRAW_NON_SYNONYMOUS_CDNA_ONLY
default: True
Flag to indicate if events which are synonymous at the cdna level should produce illustrations
drawing_width_iter_increase
type: int
environment variable: MAVIS_DRAWING_WIDTH_ITER_INCREASE
default: 500
The amount (in pixels) by which to increase the drawing width upon failure to fit
exon_min_focus_size
type: int
environment variable: MAVIS_EXON_MIN_FOCUS_SIZE
default: 10
Minimum size of an exon for it to be granted a label or min exon width
fetch_min_bin_size
type: int
environment variable: MAVIS_FETCH_MIN_BIN_SIZE
default: 50
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)
fetch_reads_bins
type: int
environment variable: MAVIS_FETCH_READS_BINS
default: 5
Number of bins to split an evidence window into to ensure more even sampling of high coverage regions
fetch_reads_limit
type: int
environment variable: MAVIS_FETCH_READS_LIMIT
default: 3000
Maximum number of reads, cap, to loop over for any given evidence window
filter_cdna_synon
type: cast_boolean
environment variable: MAVIS_FILTER_CDNA_SYNON
default: True
Filter all annotations synonymous at the cdna level
filter_min_complexity
type: float_fraction
environment variable: MAVIS_FILTER_MIN_COMPLEXITY
default: 0.2
Filter event calls based on call sequence complexity
filter_min_flanking_reads
type: int
environment variable: MAVIS_FILTER_MIN_FLANKING_READS
default: 10
Minimum number of flanking pairs for a call by flanking pairs
filter_min_linking_split_reads
type: int
environment variable: MAVIS_FILTER_MIN_LINKING_SPLIT_READS
default: 1
Minimum number of linking split reads for a call by split reads
filter_min_remapped_reads
type: int
environment variable: MAVIS_FILTER_MIN_REMAPPED_READS
default: 5
Minimum number of remapped reads for a call by contig
filter_min_spanning_reads
type: int
environment variable: MAVIS_FILTER_MIN_SPANNING_READS
default: 5
Minimum number of spanning reads for a call by spanning reads
filter_min_split_reads
type: int
environment variable: MAVIS_FILTER_MIN_SPLIT_READS
default: 5
Minimum number of split reads for a call by split reads
filter_protein_synon
type: cast_boolean
environment variable: MAVIS_FILTER_PROTEIN_SYNON
default: False
Filter all annotations synonymous at the protein level
filter_secondary_alignments
type: cast_boolean
environment variable: MAVIS_FILTER_SECONDARY_ALIGNMENTS
default: True
Filter secondary alignments when gathering read evidence
filter_trans_homopolymers
type: cast_boolean
environment variable: MAVIS_FILTER_TRANS_HOMOPOLYMERS
default: True
Filter all single bp ins/del/dup events that are in a homopolymer region of at least 3 bps and are not paired to a genomic event
flanking_call_distance
type: int
environment variable: MAVIS_FLANKING_CALL_DISTANCE
default: 50
The maximum distance allowed between breakpoint pairs (called by flanking pairs) in order for them to pair
fuzzy_mismatch_number
type: int
environment variable: MAVIS_FUZZY_MISMATCH_NUMBER
default: 1
The number of events/mismatches allowed to be considered a fuzzy match
gene1_color
type: str
environment variable: MAVIS_GENE1_COLOR
default: '#657e91'
The color of genes near the first gene
gene1_color_selected
type: str
environment variable: MAVIS_GENE1_COLOR_SELECTED
default: '#518dc5'
The color of the first gene
gene2_color
type: str
environment variable: MAVIS_GENE2_COLOR
default: '#325556'
The color of genes near the second gene
gene2_color_selected
type: str
environment variable: MAVIS_GENE2_COLOR_SELECTED
default: '#4c9677'
The color of the second gene
import_env
type: cast_boolean
environment variable: MAVIS_IMPORT_ENV
default: True
Flag to import environment variables
input_call_distance
type: int
environment variable: MAVIS_INPUT_CALL_DISTANCE
default: 20
The maximum distance allowed between breakpoint pairs (called by input tools, not validated) in order for them to pair
label_color
type: str
environment variable: MAVIS_LABEL_COLOR
default: '#000000'
The label color
limit_to_chr
type: str
environment variable: MAVIS_LIMIT_TO_CHR
default: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y']
A 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
mail_type
type: mavis.schedule.constants.MAIL_TYPE
environment variable: MAVIS_MAIL_TYPE
default: 'NONE'
accepted values: 'BEGIN', 'END', 'FAIL', 'ALL', 'NONE'
When to notify the mail_user (if given)
mail_user
type: str
environment variable: MAVIS_MAIL_USER
default: ''
User(s) to send notifications to
mask_fill
type: str
environment variable: MAVIS_MASK_FILL
default: '#ffffff'
Color of mask (for deleted region etc.)
mask_opacity
type: float_fraction
environment variable: MAVIS_MASK_OPACITY
default: 0.7
Opacity of the mask layer
masking
type: filepath
environment variable: MAVIS_MASKING
default: []
File containing regions for which input events overlapping them are dropped prior to validation
max_drawing_retries
type: int
environment variable: MAVIS_MAX_DRAWING_RETRIES
default: 5
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
max_files
type: int
environment variable: MAVIS_MAX_FILES
default: 200
The maximum number of files to output from clustering/splitting
max_orf_cap
type: int
environment variable: MAVIS_MAX_ORF_CAP
default: 3
The maximum number of orfs to return (best putative orfs will be retained)
max_proximity
type: int
environment variable: MAVIS_MAX_PROXIMITY
default: 5000
The maximum distance away from an annotation before the region in considered to be uninformative
max_sc_preceeding_anchor
type: int
environment variable: MAVIS_MAX_SC_PRECEEDING_ANCHOR
default: 6
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
memory_limit
type: int
environment variable: MAVIS_MEMORY_LIMIT
default: 16000
The maximum number of megabytes (mb) any given job is allowed
min_anchor_exact
type: int
environment variable: MAVIS_MIN_ANCHOR_EXACT
default: 6
Applies to re-aligning softclipped reads to the opposing breakpoint. the minimum number of consecutive exact matches to anchor a read to initiate targeted realignment
min_anchor_fuzzy
type: int
environment variable: MAVIS_MIN_ANCHOR_FUZZY
default: 10
Applies to re-aligning softclipped reads to the opposing breakpoint. the minimum length of a fuzzy match to anchor a read to initiate targeted realignment
min_anchor_match
type: float_fraction
environment variable: MAVIS_MIN_ANCHOR_MATCH
default: 0.9
Minimum percent match for a read to be kept as evidence
min_call_complexity
type: float_fraction
environment variable: MAVIS_MIN_CALL_COMPLEXITY
default: 0.1
The minimum complexity score for a call sequence. is an average for non-contig calls. filters low complexity contigs before alignment. see contig_complexity
min_clusters_per_file
type: int
environment variable: MAVIS_MIN_CLUSTERS_PER_FILE
default: 50
The minimum number of breakpoint pairs to output to a file
min_domain_mapping_match
type: float_fraction
environment variable: MAVIS_MIN_DOMAIN_MAPPING_MATCH
default: 0.9
A number between 0 and 1 representing the minimum percent match a domain must map to the fusion transcript to be displayed
min_double_aligned_to_estimate_insertion_size
type: int
environment variable: MAVIS_MIN_DOUBLE_ALIGNED_TO_ESTIMATE_INSERTION_SIZE
default: 2
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
min_flanking_pairs_resolution
type: int
environment variable: MAVIS_MIN_FLANKING_PAIRS_RESOLUTION
default: 10
The minimum number of flanking reads required to call a breakpoint by flanking evidence
min_linking_split_reads
type: int
environment variable: MAVIS_MIN_LINKING_SPLIT_READS
default: 2
The minimum number of split reads which aligned to both breakpoints
min_mapping_quality
type: int
environment variable: MAVIS_MIN_MAPPING_QUALITY
default: 5
The minimum mapping quality of reads to be used as evidence
min_non_target_aligned_split_reads
type: int
environment variable: MAVIS_MIN_NON_TARGET_ALIGNED_SPLIT_READS
default: 1
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
min_orf_size
type: int
environment variable: MAVIS_MIN_ORF_SIZE
default: 300
The minimum length (in base pairs) to retain a putative open reading frame (orf)
min_sample_size_to_apply_percentage
type: int
environment variable: MAVIS_MIN_SAMPLE_SIZE_TO_APPLY_PERCENTAGE
default: 10
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
min_softclipping
type: int
environment variable: MAVIS_MIN_SOFTCLIPPING
default: 6
Minimum number of soft-clipped bases required for a read to be used as soft-clipped evidence
min_spanning_reads_resolution
type: int
environment variable: MAVIS_MIN_SPANNING_READS_RESOLUTION
default: 5
Minimum number of spanning reads required to call an event by spanning evidence
min_splits_reads_resolution
type: int
environment variable: MAVIS_MIN_SPLITS_READS_RESOLUTION
default: 3
Minimum number of split reads required to call a breakpoint by split reads
novel_exon_color
type: str
environment variable: MAVIS_NOVEL_EXON_COLOR
default: '#5D3F6A'
Novel exon fill color
outer_window_min_event_size
type: int
environment variable: MAVIS_OUTER_WINDOW_MIN_EVENT_SIZE
default: 125
The minimum size of an event in order for flanking read evidence to be collected
queue
type: str
environment variable: MAVIS_QUEUE
default: ''
The queue jobs are to be submitted to
reference_genome
type: filepath
environment variable: MAVIS_REFERENCE_GENOME
default: []
Path to the human reference genome fasta file
remote_head_ssh
type: str
environment variable: MAVIS_REMOTE_HEAD_SSH
default: ''
Ssh target for remote scheduler commands
scaffold_color
type: str
environment variable: MAVIS_SCAFFOLD_COLOR
default: '#000000'
The color used for the gene/transcripts scaffolds
scheduler
type: mavis.schedule.constants.SCHEDULER
environment variable: MAVIS_SCHEDULER
default: 'SLURM'
accepted values: 'SGE', 'SLURM', 'TORQUE', 'LOCAL'
The scheduler being used
spanning_call_distance
type: int
environment variable: MAVIS_SPANNING_CALL_DISTANCE
default: 20
The maximum distance allowed between breakpoint pairs (called by spanning reads) in order for them to pair
splice_color
type: str
environment variable: MAVIS_SPLICE_COLOR
default: '#000000'
Splicing lines color
split_call_distance
type: int
environment variable: MAVIS_SPLIT_CALL_DISTANCE
default: 20
The maximum distance allowed between breakpoint pairs (called by split reads) in order for them to pair
stdev_count_abnormal
type: float
environment variable: MAVIS_STDEV_COUNT_ABNORMAL
default: 3.0
The number of standard deviations away from the normal considered expected and therefore not qualifying as flanking reads
strand_determining_read
type: int
environment variable: MAVIS_STRAND_DETERMINING_READ
default: 2
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
template_metadata
type: filepath
environment variable: MAVIS_TEMPLATE_METADATA
default: []
File containing the cytoband template information. used for illustrations only
time_limit
type: int
environment variable: MAVIS_TIME_LIMIT
default: 57600
The time in seconds any given jobs is allowed
trans_fetch_reads_limit
type: int
environment variable: MAVIS_TRANS_FETCH_READS_LIMIT
default: 12000
Related to fetch_reads_limit. overrides fetch_reads_limit for transcriptome libraries when set. if this has a value of none then fetch_reads_limit will be used for transcriptome libraries instead
trans_min_mapping_quality
type: int
environment variable: MAVIS_TRANS_MIN_MAPPING_QUALITY
default: 0
Related to min_mapping_quality. overrides the min_mapping_quality if the library is a transcriptome and this is set to any number not none. if this value is none, min_mapping_quality is used for transcriptomes aswell as genomes
trans_validation_memory
type: int
environment variable: MAVIS_TRANS_VALIDATION_MEMORY
default: 18000
Default memory limit (mb) for the validation stage (for transcriptomes)
uninformative_filter
type: cast_boolean
environment variable: MAVIS_UNINFORMATIVE_FILTER
default: False
Flag that determines if breakpoint pairs which are not within max_proximity to any annotations are filtered out prior to clustering
validation_memory
type: int
environment variable: MAVIS_VALIDATION_MEMORY
default: 16000
Default memory limit (mb) for the validation stage
width
type: int
environment variable: MAVIS_WIDTH
default: 1000
The drawing width in pixels
write_evidence_files
type: cast_boolean
environment variable: MAVIS_WRITE_EVIDENCE_FILES
default: True
Write the intermediate bam and bed files containing the raw evidence collected and contigs aligned. not required for subsequent steps but can be useful in debugging and deep investigation of events