Resource

Id: pipeline/Clinical_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

worst_effect_MANE_1.3
Type: worst_effect_MANE_1.3

Worst effect accross all transcripts.

source: worst_effect
effect_details_MANE_1.3
Type: effect_details_MANE_1.3

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

source: effect_details
gene_effects_MANE_1.3
Type: gene_effects_MANE_1.3

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
cadd_raw
Type: cadd_raw

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: cadd_phred

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
hg19_annotatable
Type: annotatable (Internal)

Lifted over allele.

source: liftover_annotatable
Annotator type: liftover_annotator

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

More info

Resource
Id: liftover/hg38ToHg19
Type: liftover_chain
Summary:
Liftover Chain Hg38 to Hg19
Resource
Id: hg38/genomes/GRCh38-hg38
Type: genome
Summary:
HG38 reference genome
Resource
Id: hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174
Type: genome
Summary:
HG19 reference genome
am_pathogenicity
Type: am_pathogenicity

AlphaMissense Pathogenicity score is a deleteriousness prediction score for missense variants

position_aggregator: mean [default]

nucleotide_aggregator: max [default]

HISTOGRAM
source: am_pathogenicity
am_class
Type: am_class

AlphaMissense Class is a deleteriousness category for missense variants

position_aggregator: concatenate [default]

nucleotide_aggregator: concatenate [default]

HISTOGRAM
source: am_class
Annotator type: np_score

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

More info

  • input_annotatable: hg19_annotatable
Resource
Id: hg19/scores/AlphaMissense
Type: np_score
Summary:
Functional impact of mutations on protein function
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
genome_gnomad_v4_af_percent
Type: genome_gnomad_v4_af_percent

Alternate allele frequency as percent

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AF_percent
genome_gnomad_v4_ac
Type: genome_gnomad_v4_ac

Alternate allele count

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AC
genome_gnomad_v4_an
Type: genome_gnomad_v4_an

Total number of alleles

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: AN
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)

Files

Filename Size md5
Clinical_annotation.yaml 3.19 KB 44cbbd7ce2a8d9fc7331d32e3d8c4f3b
genomic_resource.yaml 197.0 B 5280454238871218071863a145f600bc
statistics/