-
Notifications
You must be signed in to change notification settings - Fork 1
/
defaults.yaml
167 lines (160 loc) · 5.62 KB
/
defaults.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
dirs:
# non-normalized VCF
vcf_input_file_pattern: "{VCF_INPUT_DIR}/{{vcf_file}}"
# normalized VCF
normalized_vcf_file_pattern: "{RESULTS_DIR}/normalized_vcf/{{vcf_file}}.vcf.gz"
# Stripped-down VCF file only containing required variant information.
# Needs to be .vcf.gz to allow tabix indexing (e.g. required for random access in mmsplice)
stripped_vcf_file_pattern: "{RESULTS_DIR}/stripped_vcf/{{vcf_file}}.vcf.gz"
valid_variants_vcf_file_pattern: "{RESULTS_DIR}/valid_variants_vcf/{{vcf_file}}.vcf.gz"
# Stripped-down VCF file converted to Parquet format
vcf_pq_file_pattern: "{RESULTS_DIR}/vcf.parquet/{{vcf_file}}.parquet"
# base dir for variant effect predictions
veff_basedir: "{RESULTS_DIR}/veff"
# feature set directory
fset_dir_pattern: "{RESULTS_DIR}/fset/{{feature_set}}"
# default directory for downloaded resources
resources_dir: "{RESULTS_DIR}/resources"
isoform_proportions_tsv: "{RESOURCES_DIR}/gtex_v8_isoform_proportions.tsv"
isoform_proportions_pq: "{RESOURCES_DIR}/gtex_v8_isoform_proportions.parquet"
expected_expression_tsv: "{RESOURCES_DIR}/gtex_v8_expected_expression.tsv"
expected_expression_pq: "{RESOURCES_DIR}/gtex_v8_expected_expression.parquet"
vcf_file_endings:
- ".vcf"
- ".vcf.gz"
- ".vcf.bgz"
- ".bcf"
assembly_mapping:
hg19: "GRCh37"
hg38: "GRCh38"
vcf_header: "{SNAKEMAKE_DIR}/resources/header.vcf"
formatted_vcf_header: "{RESULTS_DIR}/header.vcf"
# gencode_basepath: "/s/genomes/Gencode/Gencode_human/release_{gencode_version}"
# MANE_select_url: 'https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/release_1.2/MANE.GRCh38.v1.2.ensembl_genomic.gtf.gz'
vep:
version: 108
vep_bin: "vep"
perl_bin: "perl"
vep_cache_dir: "{RESOURCES_DIR}/{{vep_version}}"
cadd_dir: "{RESOURCES_DIR}/{{human_genome_assembly}}"
loftee_data_dir: "{RESOURCES_DIR}/{{human_genome_assembly}}"
loftee_src_path: "{RESOURCES_DIR}/{{human_genome_assembly}}_src"
absplice:
tissue_mapping_csv: "{SNAKEMAKE_DIR}/resources/AbSplice_tissue_mapping.csv"
splicemap:
psi3: '{RESOURCES_DIR}/splicemap_{{genome}}/{{tissue}}_splicemap_psi3_method=kn_event_filter=median_cutoff.csv.gz'
psi5: '{RESOURCES_DIR}/splicemap_{{genome}}/{{tissue}}_splicemap_psi5_method=kn_event_filter=median_cutoff.csv.gz'
splicemap_tissues:
- Adipose_Subcutaneous
- Adipose_Visceral_Omentum
- Adrenal_Gland
- Artery_Aorta
- Artery_Coronary
- Artery_Tibial
- Brain_Amygdala
- Brain_Anterior_cingulate_cortex_BA24
- Brain_Caudate_basal_ganglia
- Brain_Cerebellar_Hemisphere
- Brain_Cerebellum
- Brain_Cortex
- Brain_Frontal_Cortex_BA9
- Brain_Hippocampus
- Brain_Hypothalamus
- Brain_Nucleus_accumbens_basal_ganglia
- Brain_Putamen_basal_ganglia
- Brain_Spinal_cord_cervical_c_1
- Brain_Substantia_nigra
- Breast_Mammary_Tissue
- Cells_Cultured_fibroblasts
- Cells_EBV_transformed_lymphocytes
- Colon_Sigmoid
- Colon_Transverse
- Esophagus_Gastroesophageal_Junction
- Esophagus_Mucosa
- Esophagus_Muscularis
- Heart_Atrial_Appendage
- Heart_Left_Ventricle
- Kidney_Cortex
- Liver
- Lung
- Minor_Salivary_Gland
- Muscle_Skeletal
- Nerve_Tibial
- Ovary
- Pancreas
- Pituitary
- Prostate
- Skin_Not_Sun_Exposed_Suprapubic
- Skin_Sun_Exposed_Lower_leg
- Small_Intestine_Terminal_Ileum
- Spleen
- Stomach
- Testis
- Thyroid
- Uterus
- Vagina
- Whole_Blood
use_spliceai_rocksdb: True
spliceai_rocksdb_path:
hg19: '{RESOURCES_DIR}/spliceai_rocksdb/spliceAI_hg19_chr{chromosome}.db'
hg38: '{RESOURCES_DIR}/spliceai_rocksdb/spliceAI_hg38_chr{chromosome}.db'
spliceai_rocksdb_chromosomes: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y']
models:
abexp_v1.0:
model: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.0/model.joblib"
features: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.0/features.yaml"
cutoffs:
# 50% precision, 8.5% recall:
high_confidence: 3.3951878750977413
# 20% precision, 19.1% recall:
low_confidence: 1.3049192425217895
predict_tissues:
- "Adipose - Subcutaneous"
- "Adipose - Visceral (Omentum)"
- "Adrenal Gland"
- "Artery - Aorta"
- "Artery - Coronary"
- "Artery - Tibial"
- "Brain - Amygdala"
- "Brain - Anterior cingulate cortex (BA24)"
- "Brain - Caudate (basal ganglia)"
- "Brain - Cerebellar Hemisphere"
- "Brain - Cerebellum"
- "Brain - Cortex"
- "Brain - Frontal Cortex (BA9)"
- "Brain - Hippocampus"
- "Brain - Hypothalamus"
- "Brain - Nucleus accumbens (basal ganglia)"
- "Brain - Putamen (basal ganglia)"
- "Brain - Spinal cord (cervical c-1)"
- "Brain - Substantia nigra"
- "Breast - Mammary Tissue"
- "Cells - EBV-transformed lymphocytes"
- "Cells - Cultured fibroblasts"
- "Colon - Sigmoid"
- "Colon - Transverse"
- "Esophagus - Gastroesophageal Junction"
- "Esophagus - Mucosa"
- "Esophagus - Muscularis"
- "Heart - Atrial Appendage"
- "Heart - Left Ventricle"
# - "Kidney - Cortex"
- "Liver"
- "Lung"
- "Minor Salivary Gland"
- "Muscle - Skeletal"
- "Nerve - Tibial"
- "Ovary"
- "Pancreas"
- "Pituitary"
- "Prostate"
- "Skin - Not Sun Exposed (Suprapubic)"
- "Skin - Sun Exposed (Lower leg)"
- "Small Intestine - Terminal Ileum"
- "Spleen"
- "Stomach"
- "Testis"
- "Thyroid"
- "Uterus"
- "Vagina"
- "Whole Blood"