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