Resource

Id: pipeline/Autism_annotation
Type: annotation_pipeline
Version: 0
Summary:
Description:
Labels:

Pipeline Documentation

preamble

Summary Clinical Annotation Pipeline
Description This is a pipeline to annotate with Clinical resources
Input reference genome hg38/genomes/GRCh38-hg38
Pipeline path:

Annotators

normalized_allele
Type: annotatable (Internal)

Normalized allele.

source: normalized_allele
Annotator type: normalize_allele_annotator
No description
Resource
Id: hg38/genomes/GRCh38-hg38
Type: genome
Summary:
HG38 reference genome
dbSNP_RS
Type: int

dbSNP ID (i.e. rs number)

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: RS
Annotator type: allele_score

Annotator to use with scores that depend on allele like variant frequencies, etc.

More info

  • input_annotatable: normalized_allele
Resource
Id: hg38/scores/dbSNP
Type: allele_score
Summary:
dbSNP: A public database of genetic variations for research and clinical use.
gnomad_v4_exome_ALL_af
Type: float

Alternate allele frequency

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF
Annotator type: allele_score

Annotator to use with scores that depend on allele like variant frequencies, etc.

More info

  • input_annotatable: normalized_allele
Resource
Id: hg38/variant_frequencies/gnomAD_4.1.0/exomes/ALL
Type: allele_score
Summary:
gnomAD v4.1.0 exome variants (ALL)
gnomad_v4_genome_ALL_af
Type: float

Alternate allele frequency

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF
Annotator type: allele_score

Annotator to use with scores that depend on allele like variant frequencies, etc.

More info

  • input_annotatable: normalized_allele
Resource
Id: hg38/variant_frequencies/gnomAD_4.1.0/genomes/ALL
Type: allele_score
Summary:
gnomAD v4.1.0 genome variants (ALL)
CLNSIG
Type: str

Aggregate germline classification for this single variant; multiple values are separated by a vertical bar

position_aggregator: concatenate [default]

allele_aggregator: concatenate [default]

HISTOGRAM
source: CLNSIG
Annotator type: allele_score

Annotator to use with scores that depend on allele like variant frequencies, etc.

More info

  • input_annotatable: normalized_allele
Resource
Id: hg38/scores/ClinVar_20240730
Type: allele_score
Summary:
Measure used to assess the clinical significance of genetic variants
cadd_raw
Type: float

CADD raw score for functional prediction of a SNP. The larger the score the more likely the SNP has damaging effect

position_aggregator: mean [default]

nucleotide_aggregator: max [default]

HISTOGRAM
source: cadd_raw
cadd_phred
Type: float

CADD phred-like score. This is phred-like rank score based on whole genome CADD raw scores. The larger the score the more likely the SNP has damaging effect.

position_aggregator: mean [default]

nucleotide_aggregator: max [default]

HISTOGRAM
source: cadd_phred
Annotator type: np_score

Annotator to use with genomic scores depending on genomic position and nucleotide change like CADD, MPC, etc.

More info

Resource
Id: hg38/scores/CADD_v1.4
Type: np_score
Summary:
CADD (Combined Annotation Dependent Depletion score) predicts the potential impact of a SNP
am_pathogenicity
Type: float

AlphaMissense Pathogenicity score is a deleteriousness score for missense variants

position_aggregator: mean [default]

nucleotide_aggregator: max [default]

HISTOGRAM
source: am_pathogenicity
Annotator type: np_score

Annotator to use with genomic scores depending on genomic position and nucleotide change like CADD, MPC, etc.

More info

Resource
Id: hg38/scores/AlphaMissense
Type: np_score
Summary:
Functional impact of mutations on protein function
worst_effect
Type: str

Worst effect accross all transcripts.

source: worst_effect
gene_effects
Type: str

Effects types for genes. Format: <gene_1>:<effect_1>|... A gene can be repeated.

source: gene_effects
effect_details
Type: str

Effect details for each affected transcript. Format: < transcript 1 >:<gene 1>:<effect 1>:<details 1>|...

source: effect_details
gene_list
Type: object (Internal)

List of all genes

source: gene_list
Annotator type: effect_annotator

Annotator to identify the effect of the variant on protein coding.

More info

Resource
Id: hg38/genomes/GRCh38.p13
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p13 genome assembly
Resource
Id: hg38/gene_models/GENCODE/46/basic/ALL
Type: gene_models
Summary:
GENCODE 46, basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)
worst_effect_MANE_1.3
Type: str

Worst effect accross all transcripts.

source: worst_effect
effect_details_MANE_1.3
Type: str

Effect details for each affected transcript. Format: < transcript 1 >:<gene 1>:<effect 1>:<details 1>|...

source: effect_details
gene_effects_MANE_1.3
Type: str

Effects types for genes. Format: <gene_1>:<effect_1>|... A gene can be repeated.

source: gene_effects
Annotator type: effect_annotator

Annotator to identify the effect of the variant on protein coding.

More info

Resource
Id: hg38/genomes/GRCh38.p13
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p13 genome assembly
Resource
Id: hg38/gene_models/MANE/1.3
Type: gene_models
Summary:
MANE gene model version 1.3
pLI_rank_all
Type: float

Gene rank after sorting by pLI intolerance score

gene_aggregator: dict [default]

HISTOGRAM
source: pLI_rank
pLI_rank_min
Type: float

Gene rank after sorting by pLI intolerance score

gene_aggregator: min

HISTOGRAM
source: pLI_rank
Annotator type: gene_score_annotator
No description
Resource
Id: gene_properties/gene_scores/pLI
Type: gene_score
Summary:
Probability of Loss-of-Function Intolerance
LOEUF_rank_all
Type: float

Gene ranks after sorting by LOEUF scores

gene_aggregator: dict [default]

HISTOGRAM
source: LOEUF_rank
LOEUF_rank_min
Type: float

Gene ranks after sorting by LOEUF scores

gene_aggregator: min

HISTOGRAM
source: LOEUF_rank
Annotator type: gene_score_annotator
No description
Resource
Id: gene_properties/gene_scores/LOEUF
Type: gene_score
Summary:
Degree of intolerance to predicted Loss-of-Function (pLoF) variation
Satterstrom Buxbaum Cell 2020 qval
Type: float

Multiple hypothesis adjusted p-value for gene-autism association

gene_aggregator: dict [default]

HISTOGRAM
source: Satterstrom Buxbaum Cell 2020 qval
Annotator type: gene_score_annotator
No description
Resource
Id: gene_properties/gene_scores/Satterstrom_Buxbaum_Cell_2020
Type: gene_score
Summary:
TADA derived gene-autism association score
Iossifov Wigler PNAS 2015 post noaut
Type: float

Probability of a gene to be associated with autism

gene_aggregator: dict [default]

HISTOGRAM
source: Iossifov Wigler PNAS 2015 post noaut
Annotator type: gene_score_annotator
No description
Resource
Id: gene_properties/gene_scores/Iossifov_Wigler_PNAS_2015
Type: gene_score
Summary:
Probability of a gene to be associated with autism
gene-score
Type: float

Evidence strength supporting a gene's association with autism

gene_aggregator: dict [default]

HISTOGRAM
source: gene-score
Annotator type: gene_score_annotator
No description
Resource
Id: gene_properties/gene_scores/SFARI_gene_score_2024_Q1
Type: gene_score
Summary:
SFARI gene score 2024 Q1 release
SFARI_gene_score
Type: float

Evidence strength supporting a gene's association with autism

gene_aggregator: dict [default]

HISTOGRAM
source: gene-score
Annotator type: gene_score_annotator
No description
Resource
Id: gene_properties/gene_scores/SFARI_gene_score_2024_Q1
Type: gene_score
Summary:
SFARI gene score 2024 Q1 release
autism candidates from Iossifov PNAS 2015
Type: bool

Iossifov I., et al. Low load for disruptive mutations in autism genes and their biased transmission. PNAS (2015)

source: autism candidates from Iossifov PNAS 2015
autism candidates from Sanders Neuron 2015
Type: bool

Sanders S., et. al, Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron (2015)

source: autism candidates from Sanders Neuron 2015
Yuen Scherer Nature 2017
Type: bool

List of genes (unique) from paper YuenSchererNature2017NEW, Supplementary Table 5. All damaging variants in ASD-risk genes.

source: Yuen Scherer Nature 2017
Turner Eichler ajhg 2019
Type: bool

List of genes from paper TurnerEichlerajhg2019, Supplementary mmc2 Excel file, Sheet: TableS5

source: Turner Eichler ajhg 2019
Satterstrom Buxbaum Cell 2020 top
Type: bool

List of genes (unique) from paper SatterstromBuxbaumCell_2020, Supplementary mmc2 Excel file, Sheet: 102 ASD

source: Satterstrom Buxbaum Cell 2020 top
Annotator type: gene_set_annotator

This annotator uses theautism

Resource
Id: gene_properties/gene_sets/autism
Type: gene_set
Summary:
Autism gene sets derived from publications
number_of_deletions_in_SSC_affected
Type: int

The number of CNVs overlapping with the annotatable.

source: count
Annotator type: cnv_collection
No description
Resource
Id: hg38/cnv_collections/Iossifov_Lab_SSC_AGRE_2021
Type: cnv_collection
number_of_duplications_in_SSC_affected
Type: int

The number of CNVs overlapping with the annotatable.

source: count
Annotator type: cnv_collection
No description
Resource
Id: hg38/cnv_collections/Iossifov_Lab_SSC_AGRE_2021
Type: cnv_collection
in_a_SFARI_gene_CNV
Type: int

The number of CNVs overlapping with the annotatable.

source: count
Annotator type: cnv_collection
No description
Resource
Id: hg38/cnv_collections/SFARI_gene_CNV
Type: cnv_collection
Summary:
SFARI_Gene CNV collection

Files

Filename Size md5
Autism_annotation.yaml 3.41 KB 03e1f7d09d7343c639389fa28ae70051
genomic_resource.yaml 199.0 B 9cecef9a85a7aee31786fcbee7961253
statistics/