Index

Symbols

2bit

A

aligner, [1] aligner_reference, [1] annotation_figure annotation_figure_legend annotation_filters, [1] annotation_id annotation_memory, [1] annotations, [1]

assembly_kmer_size, [1] assembly_max_paths, [1] assembly_min_edge_trim_weight, [1] assembly_min_exact_match_to_remap, [1] assembly_min_remap_coverage, [1] assembly_min_remapped_seq, [1] assembly_min_uniq, [1] assembly_strand_concordance, [1]

B

BAM bed blat blat_limit_top_aln, [1] blat_min_identity, [1] break1_chromosome break1_ewindow break1_ewindow_count break1_ewindow_practical_coverage break1_homologous_seq break1_orientation break1_position_end break1_position_start break1_seq break1_split_reads break1_split_reads_forced break1_strand

break2_chromosome break2_ewindow break2_ewindow_count break2_ewindow_practical_coverage break2_homologous_seq break2_orientation break2_position_end break2_position_start break2_seq break2_split_reads break2_split_reads_forced break2_strand BreakDancer breakpoint breakpoint pair breakpoint_color, [1] BreakSeq BWA

C

call_error, [1] call_method call_sequence_complexity cdna_synon Chimerascan clean_aligner_files, [1] cluster_id cluster_initial_size_limit, [1] cluster_radius, [1] cluster_size CNVnator concurrency_limit, [1] contig_alignment_cigar contig_alignment_query_name contig_alignment_reference_start contig_alignment_score

contig_aln_max_event_size, [1] contig_aln_merge_inner_anchor, [1] contig_aln_merge_outer_anchor, [1] contig_aln_min_anchor_size, [1] contig_aln_min_extend_overlap, [1] contig_aln_min_query_consumption, [1] contig_aln_min_score, [1] contig_build_score contig_call_distance, [1] contig_remap_coverage contig_remap_score contig_remapped_read_names contig_remapped_reads contig_seq contig_strand_specific contigs_aligned contigs_assembled

D

DeFuse DELLY dgv_annotation, [1] domain_color, [1] domain_mismatch_color, [1]

domain_name_regex_filter, [1] domain_scaffold_color, [1] draw_fusions_only, [1] draw_non_synonymous_cdna_only, [1] drawing_width_iter_increase, [1]

E

event event type

event_type exon_min_focus_size, [1]

F

fasta fetch_min_bin_size, [1] fetch_reads_bins, [1] fetch_reads_limit, [1] filter_cdna_synon, [1] filter_min_complexity, [1] filter_min_flanking_reads, [1] filter_min_linking_split_reads, [1] filter_min_remapped_reads, [1] filter_min_spanning_reads, [1] filter_min_split_reads, [1] filter_protein_synon, [1] filter_secondary_alignments, [1] filter_trans_homopolymers, [1]

flanking read pair flanking_call_distance, [1] flanking_median_fragment_size flanking_pairs flanking_pairs_compatible flanking_stdev_fragment_size fusion_cdna_coding_end, [1] fusion_cdna_coding_start fusion_mapped_domains fusion_protein_hgvs fusion_sequence_fasta_file fusion_sequence_fasta_id fusion_splicing_pattern fuzzy_mismatch_number, [1]

G

gene1 gene1_aliases gene1_color, [1] gene1_color_selected, [1] gene1_direction gene2 gene2_aliases gene2_color, [1]

gene2_color_selected, [1] gene2_direction gene_product_type genes_encompassed genes_overlapping_break1 genes_overlapping_break2 genes_proximal_to_break1 genes_proximal_to_break2

H

half-mapped read

HGVS

I

IGV IGV batch file

import_env, [1] inferred_pairing input_call_distance, [1]

J

JSON

L

label_color, [1] library

limit_to_chr, [1] linking_split_reads

M

mail_type, [1] mail_user, [1] Manta mask_fill, [1] mask_opacity, [1] masking, [1] mavis (module) mavis.annotate (module) mavis.bam (module) mavis.cluster (module) mavis.illustrate (module) mavis.pairing (module) mavis.schedule (module) mavis.summary (module) mavis.validate (module) max_drawing_retries, [1] max_files, [1] max_orf_cap, [1]

max_proximity, [1] max_sc_preceeding_anchor, [1] memory_limit, [1] min_anchor_exact, [1] min_anchor_fuzzy, [1] min_anchor_match, [1] min_call_complexity, [1] min_clusters_per_file, [1] min_domain_mapping_match, [1] min_double_aligned_to_estimate_insertion_size, [1] min_flanking_pairs_resolution, [1] min_linking_split_reads, [1] min_mapping_quality, [1] min_non_target_aligned_split_reads, [1] min_orf_size, [1] min_sample_size_to_apply_percentage, [1] min_softclipping, [1] min_spanning_reads_resolution, [1] min_splits_reads_resolution, [1]

N

net_size

novel_exon_color, [1]

O

opposing_strands

outer_window_min_event_size, [1]

P

pairing Pindel product_id

protein_synon protocol psl pslx

Q

queue, [1]

R

raw_break1_split_reads raw_break2_split_reads raw_flanking_pairs

raw_spanning_reads reference_genome, [1] remote_head_ssh, [1]

S

scaffold_color, [1] scheduler, [1] SGE SLURM spanning read spanning_call_distance, [1] spanning_read_names spanning_reads splice_color, [1] split read

split_call_distance, [1] STAR-Fusion stdev_count_abnormal, [1] strand_determining_read, [1] stranded Strelka structural variant supplementary_call SV SVG

T

template_metadata, [1] time_limit, [1] tools TORQUE tracking_id

Trans-ABySS trans_fetch_reads_limit, [1] trans_min_mapping_quality, [1] trans_validation_memory, [1] transcript1 transcript2

U

uninformative_filter, [1]

untemplated_seq

V

validation_id

validation_memory, [1]

W

width, [1]

write_evidence_files, [1]