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Resource

Id pipeline/Autism_annotation
Type annotation_pipeline
Version 0
Summary
Description
Labels

Pipeline Documentation

preamble

Summary Autism Annotation Pipeline
Description This is a pipeline to annotate with autism related attributes.
Input reference genome hg38/genomes/GRCh38.p14
Pipeline path:

Annotators

worst_effect
Type:

Worst effect across all transcripts.

source: worst_effect
gene_effects
Type:

<gene_1>:<effect_1>|... A gene can be repeated.

source: gene_effects
effect_details
Type:

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

source: effect_details
gene_list
Type: (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.p14
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p14 genome assembly
Resource
Id: hg38/gene_models/GENCODE/48/basic/PRI
Type: gene_models
Summary:
GENCODE 48, basic gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions
worst_effect_MANE_1.4
Type:

Worst effect across all transcripts.

source: worst_effect
effect_details_MANE_1.4
Type:

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

source: effect_details
gene_effects_MANE_1.4
Type:

<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.p14
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p14 genome assembly
Resource
Id: hg38/gene_models/MANE/1.4
Type: gene_models
Summary:
MANE gene model version 1.4
normalized_allele
Type: (Internal)

Normalized allele.

source: normalized_allele
Annotator type: normalize_allele_annotator
No description
Resource
Id: hg38/genomes/GRCh38.p14
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p14 genome assembly
dbSNP_RS
Type:

dbSNP ID (i.e. rs number)

position_aggregator: list [default]

allele_aggregator: list [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_exomes_ALL_af
Type:

Alternate allele frequency

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF
gnomad_v4_exomes_ALL_af_percent
Type:

Alternate allele frequency as percent

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF_percent
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_genomes_ALL_af
Type:

Alternate allele frequency

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF
gnomad_v4_genomes_ALL_af_percent
Type:

Alternate allele frequency as percent

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF_percent
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:

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

position_aggregator: list [default]

allele_aggregator: list [default]

HISTOGRAM
source: CLNSIG
CLNDN
Type:

ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB

position_aggregator: list [default]

allele_aggregator: list [default]

HISTOGRAM
source: CLNDN
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
phylop100way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phyloP100way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phyloP100way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 100 species
phylop30way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phyloP30way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phyloP30way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 30 species
phylop20way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phyloP20way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phyloP20way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 20 species
phylop7way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phyloP7way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phyloP7way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 7 species
phastcons100way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phastCons100way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phastCons100way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 100 species
phastcons30way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phastCons30way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phastCons30way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 30 species
phastcons20way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phastCons20way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phastCons20way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 20 species
phastcons7way
Type:

The score is a number that reflects the conservation at a position.

position_aggregator: mean [default]

HISTOGRAM
source: phastCons7way
Annotator type: position_score

Annotator to use with genomic scores depending on genomic position like phastCons, phyloP, FitCons2, etc.

More info

Resource
Id: hg38/scores/phastCons7way
Type: position_score
Summary:
Conservation score based on the multiple alignment of 7 species
cadd_raw
Type:

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]

allele_aggregator: max [default]

HISTOGRAM
source: cadd_raw
cadd_phred
Type:

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]

allele_aggregator: max [default]

HISTOGRAM
source: cadd_phred
Annotator type: allele_score

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

More info

Resource
Id: hg38/scores/CADD_v1.7
Type: allele_score
Summary:
CADD (Combined Annotation Dependent Depletion score) predicts the potential impact of a SNP
am_pathogenicity
Type:

AlphaMissense Pathogenicity score is a deleteriousness score for missense variants

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: am_pathogenicity
Annotator type: allele_score

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

More info

Resource
Id: hg38/scores/AlphaMissense
Type: allele_score
Summary:
Functional impact of mutations on protein function
hg19_annotatable
Type: (Internal)

The lifted over annotatable

source: liftover_annotatable
Annotator type: liftover_annotator

Annotator to lift over a variant from one reference genome to another.

More info

Resource
Id: liftover/hg38_to_hg19
Type: liftover_chain
Summary:
Liftover Chain Hg38 to Hg19
Resource
Id: hg38/genomes/GRCh38.p14
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p14 genome assembly
Resource
Id: hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174
Type: genome
Summary:
HG19 reference genome
mpc
Type:

Missense badness, PolyPhen-2, and Constraint. A deleteriousness prediction score for missense variants"

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: MPC
Annotator type: allele_score

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

More info

  • input_annotatable: hg19_annotatable
Resource
Id: hg19/scores/MPC
Type: allele_score
Summary:
MPC (Missense badness, PolyPhen-2, and Constraint) is a composite score that predicts the impact of missense variants.
pLI_rank_all
Type:

Gene rank after sorting by pLI intolerance score

gene_aggregator: dict [default]

HISTOGRAM
source: pLI_rank
pLI_rank_min
Type:

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:

Gene ranks after sorting by LOEUF scores

gene_aggregator: dict [default]

HISTOGRAM
source: LOEUF_rank
LOEUF_rank_min
Type:

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:

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:

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
SFARI_gene_score
Type:

Evidence strength supporting a gene's association with autism

gene_aggregator: dict [default]

HISTOGRAM
source: SFARI 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:

(239) 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:

(65) 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:

(55) 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:

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

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

(102) 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 gene set collection annotator uses the autism gene set collection.

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

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
Summary:
De novo CNVs from SSC and AGRE WGS
number_of_duplications_in_SSC_affected
Type:

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
Summary:
De novo CNVs from SSC and AGRE WGS
in_a_SFARI_gene_CNV
Type:

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 4.15 KB c8df7d0a49168c216c32538736476c90
genomic_resource.yaml 199.0 B 9cecef9a85a7aee31786fcbee7961253
statistics/