cnaster/sim_config.yaml at main · michaelJwilson/cnaster · GitHub

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paths:
  sample_sheet: None
  output_dir : /u/mw9568/scratch/cnaster/simulated_example/results/
  cache_dir : /n/fs/scratch/mw9568/cnaster/.cache

# tumorprop_file : /n/fs/scratch/mw9568/cnaster/loh_estimator_tumor_prop.tsv
preprocessing:
  normalidx_file : None
  tumorprop_file : None

run:
  bafonly : False

references:
  geneticmap_file : /u/mw9568/research/data/references/genetic_map_GRCh38_merged.tab.gz
  hgtable_file : /u/mw9568/research/data/references/hgTables_hg38_gencode.txt
  filtergenelist_file : /u/mw9568/research/data/references/ig_gene_list.txt
  filterregion_file : /u/mw9568/research/data/references/HLA_regions.bed

quality:
  secondary_min_umi : 300

# TODO HACK npart_phasing : 3 -> 1
phasing:
  nu : 1.0
  logphase_shift : -2.0
  npart_phasing : 1

# TODO HACK max_iter_outer : 20 ->
#           spatial_weight : 1.0 ->
hmrf:
  n_clones : 3
  n_clones_rdr : 2
  min_spots_per_clone : 100
  min_avgumi_per_clone : 10
  maxspots_pooling : 7
  tumorprop_threshold : 0.5
  max_iter_outer : 20
  nodepotential : max
  initialization_method : rectangle
  num_hmrf_initialization_start : 0
  num_hmrf_initialization_end : 1
  spatial_weight : 1.0
  inertia : 0
  construct_adjacency_method : hexagon
  construct_adjacency_w : 1.0

# TODO HACK max_iter : 30 ->
#           solver: nm ->
#           t: 0.99999 ->
#           tol: 0.0001 ->
hmm:
  solver: "L-BFGS-B"
  n_states : 7
  params : smp
  t : 0.99999
  t_phaseing : 0.99999
  fix_NB_dispersion : False
  shared_NB_dispersion : True
  fix_BB_dispersion : False
  shared_BB_dispersion : True
  compression_decimals: 3
  max_iter : 30
  tol : 0.001
  gmm_random_state : 0
  gmm_maxiter: 30
  np_threshold : 1.0
  np_eventminlen : 10
  em_maxiter: 1500
  em_xtol: 1e-4
  em_ftol: 1e-4
  em_xrtol: 1e-4
  em_disp: 0

# NB N sub-set of states will use the first N
nbinom:
  start_params: 0.1,0.1,0.1,0.1,0.1,0.1,0.1
  start_disp: 1.0e-2

# TODO HACK start_disp: 1 ->
betabinom:
  start_params: 0.5,0.5,0.5,0.5,0.5,0.5,0.5
  start_disp:  20.0

# TODO HACK ploidy : "diploid,triploid,tetraploid" ->
int_copy_num:
  nonbalance_bafdist : 1.0
  nondiploid_rdrdist : 10.0
  ploidy : "diploid"