tools.yaml

sv_tools_enabled:
  - "sniffles"

aligner: "ngmlr"

tools:
  tmp_dir: ""
  samtools:
    path: "samtools"
    threads: 100
    mem_mb_per_thread: 1000
    mem_mb_core: 2000
  ngmlr:
    reads_cnt_per_run: 200000
    path: "ngmlr"
    threads: 100
    time: "72:0:0"
    mem_mb_per_thread: 1000
    mem_mb_core: 6000
  sniffles:
    path: "sniffles"
    threads: 5
    min_support: 2
    min_length: 20
    max_num_splits: 10
    max_distance: 50
    num_reads_report: -1
    min_seq_size: 1000
    time: "24:0:0"
    mem_mb_per_thread: 1000
    mem_mb_core: 25000
  java:
    path: "java"
  jasmine:
    src_path: ""
    threads: 2
    mem_mb_core: 20000
    mem_mb_per_thread: 4000
    ins_to_dup:
      max_dup_length: 10000
      script_name: "InsertionsToDuplications"
    specific_marked:
      spec_reads_fixed: 10
      spec_reads_fraction: 0.25
      spec_len: 30
    is_merging:
      normalize_types: True
      use_types: True
      use_strands: True
      use_edit_distance: False
      use_end: False
      max_distance: 100
      min_distance: -1
      threads: 100
      strategy: "default"
      kd_tree_norm: 2
      min_seq_id: 0
      max_distance_linear: 0
      k_jaccard: 9
  iris:
    src_path: ""
    threads: 100
    mem_mb_core: 20000
    mem_mb_per_thread: 1000
    min_ins_length: 30
    max_out_length: 100000
    max_ins_dist: 100
    max_length_change: 0.25
  minimap2:
    reads_cnt_per_run: 800000
    mem_mb_per_thread: 1000
    mem_mb_core: 6000
    path: "minimap2"
    threads: 100
    time: "72:0:0"
  racon:
    path: "racon"
  sv_sizes:
    path: "sv_sizes.py"
    bins: "1,30,50,100,150,200,350,300,500,750,1000,2000,5000,10000,50000,100000,500000"
    types: "INS,DEL,DUP,INV,TRA"
    abs_length: True
    info_length_field: "SVLEN"
  sam_fix:
    path: "fix_sam.py"
  seqtk:
    path: "seqtk"
  mosdepth:
    path: "mosdepth"
    mem_mb_per_thread: 1000
    mem_mb_core: 2000
    threads: 100
    paer_base: False
    fast_mode: True
    window_size: 500
  meryl:
    path: "meryl"
    distinct: 0.9998
    k: 15
  winnowmap:
    reads_cnt_per_run: 800000
    mem_mb_per_thread: 1000
    mem_mb_core: 6000
    path: "winnowmap"
    threads: 100
    time: "72:0:0"