Resource

Id: pipeline/T2T_Clinical_annotation
Type: annotation_pipeline
Version: 0
Summary:
Description:
Labels:

Pipeline Documentation

preamble

Summary Annotates t2t coordinates with Clinical resources
Description This is a pipeline to annotate variants from t2t assembly with Clinical resources
Input reference genome t2t/genomes/t2t-chm13v2.0
Pipeline path:

Annotators

hg38_annotatable
Type: annotatable (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/T2T_to_hg38
Type: liftover_chain
Summary:
Liftover Chain T2T to Hg38
Resource
Id: t2t/genomes/t2t-chm13v2.0
Type: genome
Summary:
Nucleotide sequence of the T2T-CHM13v2.0 genome assembly
Resource
Id: hg38/genomes/GRCh38.p14
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p14 genome assembly
normalized_allele
Type: annotatable (Internal)

Normalized allele.

source: normalized_allele
Annotator type: normalize_allele_annotator
  • input_annotatable: hg38_annotatable
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
CLNDN
Type: str

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
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]

allele_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]

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

  • input_annotatable: normalized_allele
Resource
Id: hg38/scores/CADD_v1.4
Type: allele_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]

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

  • input_annotatable: normalized_allele
Resource
Id: hg38/scores/AlphaMissense
Type: allele_score
Summary:
Functional impact of mutations on protein function
hg19_annotatable
Type: annotatable (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/T2T_to_hg19
Type: liftover_chain
Summary:
Liftover Chain T2T to Hg19
Resource
Id: t2t/genomes/t2t-chm13v2.0
Type: genome
Summary:
Nucleotide sequence of the T2T-CHM13v2.0 genome assembly
Resource
Id: hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174
Type: genome
Summary:
HG19 reference genome
mpc
Type: float

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.
worst_effect_GENCODE_48
Type: str

Worst effect accross all transcripts.

source: worst_effect
effect_details_GENCODE_48
Type: str

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

source: effect_details
gene_effects_GENCODE_48
Type: str

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

source: gene_effects
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

  • input_annotatable: normalized_allele
Resource
Id: hg38/genomes/GRCh38.p13
Type: genome
Summary:
Nucleotide sequence of the GRCh38.p13 genome assembly
Resource
Id: hg38/gene_models/GENCODE/48/basic/ALL
Type: gene_models
Summary:
GENCODE 48, 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

<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

  • input_annotatable: normalized_allele
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: object

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: object

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
worst_effect
Type: str

Worst effect accross all transcripts.

source: worst_effect
gene_effects
Type: str

<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
Annotator type: effect_annotator

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

More info

Resource
Id: t2t/genomes/t2t-chm13v2.0
Type: genome
Summary:
Nucleotide sequence of the T2T-CHM13v2.0 genome assembly
Resource
Id: t2t/gene_models/ncbiRefSeq_110
Type: gene_models
Summary:
NCBI RefSeq 110, comprehensive gene annotation on the T2T-CHM13v2.0 assembly (gapless chromosomes, no alternate scaffolds).

Files

Filename Size md5
T2T_Clinical_annotation.yaml 2.74 KB d58c7d2d34783e3af540b6ed64620735
genomic_resource.yaml 248.0 B b306c019c5273e951bc54e05307fdb21
statistics/