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config.yaml
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config.yaml
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# ============================= AbSplice-DNA related ================================
# specify genome version hg19 or hg38
genome: hg19
# choose if the additional information from SpliceAI and SpliceMaps columns are required in the AbSplice-DNA output
extra_info_dna: True
# store all the vcf file that you want to analyze to directory ../data/resources/vcf_files/
vcf: ../data/resources/analysis_files/vcf_files/{vcf_id}
# parameters for variant filtering
variant_filtering:
minor_allele_frequency:
apply_filter: True
filter_cutoff: 0.001
max_num_samples:
apply_filter: True
filter_cutoff: 2
# False by default, you can change this if you want to run on large datasets (see Readme)
use_rocksdb: False
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
# ============================= AbSplice-RNA related ================================
AbSplice_RNA: False
# choose if the additional information from SpliceAI and SpliceMaps columns are required in the AbSplice-RNA output
extra_info_rna: True
DROP:
geneAnnotation: 'v29'
DROP_group:
- 'Cells_Cultured_fibroblasts'
working_dir: ../data/resources/analysis_files/absplice_rna_related_files/DROP/
sample_annotation: processed_data/aberrant_splicing/annotations/{tissue_cat}.tsv
count_table: processed_data/aberrant_splicing/datasets/
outliers: processed_results/aberrant_splicing/results/{geneAnnotation}/
cat_outlier_filtering:
padjustGene_cutoff: 0.1
padjust_junction_cutoff: 0.05
totalCounts_cutoff: 20
delta_psi_cutoff: 0.3
outlier_type: 'psi5__psi3__theta'