- 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'
- aligner_reference
filepath - Path to the aligner reference file used for aligning the contig sequences. The corresponding environment variable is MAVIS_ALIGNER_REFERENCE and the default value is None
- 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
- annotations
filepath - Path to the reference annotations of genes, transcript, exons, domains, etc. The corresponding environment variable is MAVIS_ANNOTATIONS and the default value is []
- assembly_kmer_size
float_fraction - The percent of the read length to make kmers for assembly. The corresponding environment variable is MAVIS_ASSEMBLY_KMER_SIZE and the default value is 0.74
- 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 8
- assembly_min_edge_trim_weight
int - 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. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_EDGE_TRIM_WEIGHT and the default value is 3
- 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_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_uniq
float_fraction - Minimum percent uniq required to keep separate assembled contigs. if contigs are more similar then the lower scoring, then shorter, contig is dropped. The corresponding environment variable is MAVIS_ASSEMBLY_MIN_UNIQ and the default value is 0.1
- 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
- clean_aligner_files
bool - 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. The corresponding environment variable is MAVIS_CLEAN_ALIGNER_FILES and the default value is False
- 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
- concurrency_limit
int - The concurrency limit for tasks in any given job array or the number of concurrent processes allowed for a local run. The corresponding environment variable is MAVIS_CONCURRENCY_LIMIT and the default value is None
- 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 10
- dgv_annotation
filepath - Path to the dgv reference processed to look like the cytoband file. The corresponding environment variable is MAVIS_DGV_ANNOTATION and the default value is []
- 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
- exon_min_focus_size
int - Minimum size of an exon for it to be granted a label or min exon width. The corresponding environment variable is MAVIS_EXON_MIN_FOCUS_SIZE and the default value is 10
- 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_complexity
float_fraction - Filter event calls based on call sequence complexity. The corresponding environment variable is MAVIS_FILTER_MIN_COMPLEXITY and the default value is 0.2
- 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 False
- 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
- filter_trans_homopolymers
bool - 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. The corresponding environment variable is MAVIS_FILTER_TRANS_HOMOPOLYMERS 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 50
- 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 20
- label_color
str - The label color. The corresponding environment variable is MAVIS_LABEL_COLOR and the default value is '#000000'
- limit_to_chr
str - 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. 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']
- mail_type
MAIL_TYPE - When to notify the mail_user (if given). The corresponding environment variable is MAVIS_MAIL_TYPE and the default value is 'NONE'. Accepted values include: 'BEGIN', 'END', 'FAIL', 'ALL', 'NONE'
- mail_user
str - User(s) to send notifications to. The corresponding environment variable is MAVIS_MAIL_USER and the default value is ''
- 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
- masking
filepath - File containing regions for which input events overlapping them are dropped prior to validation. The corresponding environment variable is MAVIS_MASKING and the default value is []
- 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 5
- 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 targeted 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 targeted 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_call_complexity
float_fraction - The minimum complexity score for a call sequence. is an average for non-contig calls. filters low complexity contigs before alignment. see contig_complexity. The corresponding environment variable is MAVIS_MIN_CALL_COMPLEXITY and the default value is 0.1
- 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 base pairs) 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 '#5D3F6A'
- 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 ''
- reference_genome
filepath - Path to the human reference genome fasta file. The corresponding environment variable is MAVIS_REFERENCE_GENOME and the default value is []
- remote_head_ssh
str - Ssh target for remote scheduler commands. The corresponding environment variable is MAVIS_REMOTE_HEAD_SSH 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', 'TORQUE', 'LOCAL'
- 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 20
- 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 20
- 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
- template_metadata
filepath - File containing the cytoband template information. used for illustrations only. The corresponding environment variable is MAVIS_TEMPLATE_METADATA and the default value is []
- 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_fetch_reads_limit
int - 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. The corresponding environment variable is MAVIS_TRANS_FETCH_READS_LIMIT and the default value is 12000
- trans_min_mapping_quality
int - 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. The corresponding environment variable is MAVIS_TRANS_MIN_MAPPING_QUALITY and the default value is 0
- 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 False
- 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
- write_evidence_files
bool - 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. The corresponding environment variable is MAVIS_WRITE_EVIDENCE_FILES and the default value is True