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default_config.yml
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default_config.yml
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alignment:
# Default is no substitution_matrix, can use any substitution_matrix from (from Bio.SubsMat import MatrixInfo)
# e.g. substitution_matrix: "blosum62"
substitution_matrix: ""
match_score: 5 # match score. 5 is EMBOSS needle default
mismatch_score: -4 # mismatch score. -4 is EMBOSS needle default
open_gap_score: -25 # open_gap_score score. -10 is EMBOSS needle default
extend_gap_score: 0 # extend_gap_score score. -0.5 is EMBOSS needle default
NHEJ_inference:
max_indel_size: &max_indel_size 500 # Max indel size, 500 is account as "infinity"
window_size: 10 # Priors size should be 2*window_size for deletions & substitutions a 2*window_size+1 for insertions
default_q: 0.93 # the probability of an indel to occur through an edit event if user specifies --override_noise_estimation
IndelTypes:
Deletions:
del_len_1:
min: 1 # min indel length
max: 1 # max indel length
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
del_len_2:
min: 2
max: 2
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
del_len_3:
min: 3
max: 3
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
del_len_4:
min: 4
max: 4
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
del_len_5:
min: 5
max: 5
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
del_len_6_to_max:
min: 6
max: *max_indel_size
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
Insertions:
ins_len_1:
min: 1
max: 1
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
ins_len_2:
min: 2
max: 2
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
ins_len_3:
min: 3
max: 3
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
ins_len_4:
min: 4
max: 4
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
ins_len_5:
min: 5
max: 5
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
ins_len_6_to_max:
min: 6
max: *max_indel_size
pos_prior: [0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.1, 0.5,
0.1, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001]
Substitutions:
sub:
min: 1
max: *max_indel_size
pos_prior: [0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.01,
0.01, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001]
Mixed: # Any combination of adjacent insertion, deletion and/or Substitution
mixed_len_1:
min: 1
max: 1
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
mixed_len_2:
min: 2
max: 2
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
mixed_len_3:
min: 3
max: 3
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
mixed_len_4:
min: 4
max: 4
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
mixed_len_5:
min: 5
max: 5
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
mixed_len_6_to_max:
min: 6
max: *max_indel_size
pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]