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defaults.yaml
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defaults.yaml
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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']
enformer:
batch_size: 2
isoform_aggregation_mode: canonical
variant_upstream_tss: 50
variant_downstream_tss: 200
# Whether to calculate the variant effect only for the canonical transcripts
canonical_only: true
# Whether to calculate the variant effect only for the protein coding transcripts
protein_coding_only: true
# the chromosomes in which to look for transcripts
chromosomes: ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12",
"chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY" ]
# How many central bins to average over?
num_agg_central_bins: 3
# Enformer will be run 3 times, once centered on the TSS, and +-<shift> from the TSS
shift: 43
# How many bins to save from each run. A smaller number will save space, since
# we only care about the central bins (close to the TSS)
num_output_bins: 21
tissue_mapper_pkl: "{SNAKEMAKE_DIR}/resources/enformer/tissue_mapper.pkl"
tracks_yml: "{SNAKEMAKE_DIR}/resources/enformer/tracks.yaml"
# Whether to download the reference or generate them locally
download_reference: true
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:
high_confidence: 3.3951878750977413
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"
abexp_v1.1_nobcv:
model: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.1_nobcv/model.joblib"
features: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.1_nobcv/features.yaml"
cutoffs:
high_confidence: 3.83833533874002
low_confidence: 1.63628553283956
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"
abexp_v1.1:
model: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.1/model.joblib"
features: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.1/features.yaml"
cutoffs:
high_confidence: 3.83833533874002
low_confidence: 1.63628553283956
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"
abexp_v1.1_Enformer:
model: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.1_Enformer/model.joblib"
features: "{SNAKEMAKE_DIR}/resources/models/abexp_v1.1_Enformer/features.yaml"
cutoffs:
high_confidence: 3.83833533874002
low_confidence: 1.63628553283956
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"