Resource

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

Pipeline Documentation

preamble

Summary Demo pipeline
Description Demonstrates a GAIn pipeline
Input reference genome hg38/genomes/GRCh38-hg38
Pipeline path:

Annotators

worst_effect
Type:

Worst effect accross all transcripts.

source: worst_effect
gene_list
Type: (Internal)

List of all genes

source: gene_list
genes
Type:

Comma separated list of all affected genes.

source: genes
Annotator type: effect_annotator

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

More info

Resource
Id: hg38/genomes/GRCh38-hg38
Type: genome
Summary:
HG38 reference genome
Resource
Id: hg38/gene_models/MANE/1.3
Type: gene_models
Summary:
MANE gene model version 1.3
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
normalized_allele
Type: (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
gnomAD_4.1_af
Type:

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)
MVP_rankscore
Type:

MVP scores were ranked among all MVP scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MVP scores in dbNSFP.

position_aggregator: mean [default]

allele_aggregator: max [default]

HISTOGRAM
source: MVP_rankscore
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/dbNSFP4.9a
Type: allele_score
Summary:
dbNSFPv4.9a
CLNSIG
Type:

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
CLNDN
Type:

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

position_aggregator: concatenate [default]

allele_aggregator: concatenate [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
pLI_rank
Type:

Gene rank after sorting by pLI intolerance score

gene_aggregator: dict [default]

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
replication fork processing
Type:

replicationforkprocessing

source: GO:0031297
Annotator type: gene_set_annotator

This gene set collection annotator uses the GO gene set collection.

Resource
Id: gene_properties/gene_sets/GO_2024-06-17_release
Type: gene_set_collection
Summary:
GO terms 2024-06-17 release
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/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
FitCons2_E063
Type:

Adipose Nuclei Score (E063)

position_aggregator: mean [default]

HISTOGRAM
source: FitCons2_E063
Annotator type: position_score

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

More info

  • input_annotatable: hg19_annotatable
Resource
Id: hg19/scores/fitCons2/E063
Type: position_score
Summary:
Cell-type specific FitCons scores for Adipose Nuclei (E063)

Files

Filename Size md5
Paper_pipeline.yaml 1.39 KB dbb8df33c339024c42e7b589e529b22a
genomic_resource.yaml 482.0 B d746b1b4c60a7c2cf465dc2aed395630
statistics/