Resource
| Id | pipeline/hg19_clinical_annotation |
|---|---|
| Type | annotation_pipeline |
| Version | 0 |
| Summary |
Clinical Annotation Pipeline for hg19
|
| Description |
This is a pipeline to annotate variants in hg19 assembly with Clinical resources. |
| Labels |
Pipeline Documentation
preamble
| Summary | Clinical Annotation Pipeline for hg19 |
|---|---|
| Description | This is a pipeline to annotate hg19 variants with Clinical resources |
| Input reference genome | hg19/genomes/GATK_ResourceBundle_5777_b37_phiX174 |
Annotators
The lifted over annotatable
Annotator to lift over a variant from one reference genome to another.
Worst effect across all transcripts.
Effect details for each affected transcript. Format: < transcript 1 >:<gene 1>:<effect 1>:<details 1>|...
<gene_1>:<effect_1>|... A gene can be repeated.
Annotator to identify the effect of the variant on protein coding.
- input_annotatable:
hg38_annotatable
Normalized allele.
- input_annotatable:
hg38_annotatable
dbSNP ID (i.e. rs number)
allele_aggregator: list [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
- input_annotatable:
normalized_allele
Alternate allele frequency
allele_aggregator: max [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
- input_annotatable:
normalized_allele
Alternate allele frequency
allele_aggregator: max [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
- input_annotatable:
normalized_allele
ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB
allele_aggregator: list [default]
Aggregate germline classification for this single variant; multiple values are separated by a vertical bar
allele_aggregator: list [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
- input_annotatable:
normalized_allele
CADD raw score for functional prediction of a SNP. The larger the score the more likely the SNP has damaging effect
allele_aggregator: max [default]
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.
allele_aggregator: max [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
- input_annotatable:
normalized_allele
AlphaMissense Pathogenicity score is a deleteriousness score for missense variants
allele_aggregator: max [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
- input_annotatable:
normalized_allele
Missense badness, PolyPhen-2, and Constraint. A deleteriousness prediction score for missense variants"
allele_aggregator: max [default]
Annotator to use with scores that depend on allele like variant frequencies, etc.
Mode (mode parameter, applies to VCFAllele inputs only):
allele(default): exact chrom/pos/ref/alt match.region: aggregates scores for all allele lines overlapping the annotatable's span.
Non-VCFAllele annotatables always use region aggregation.
Worst effect across all transcripts.
<gene_1>:<effect_1>|... A gene can be repeated.
Effect details for each affected transcript. Format: < transcript 1 >:<gene 1>:<effect 1>:<details 1>|...
List of all genes
Annotator to identify the effect of the variant on protein coding.
- input_annotatable:
hg38_annotatable
Gene rank after sorting by pLI intolerance score
gene_aggregator: dict [default]
Gene rank after sorting by pLI intolerance score
gene_aggregator: min
Gene ranks after sorting by LOEUF scores
gene_aggregator: dict [default]
Gene ranks after sorting by LOEUF scores
gene_aggregator: min
Files
| Filename | Size | md5 |
|---|---|---|
| genomic_resource.yaml | 237.0 B | 017d52601123d47861ab227ab04d18a3 |
| hg19_clinical_annotation.yaml | 2.37 KB | cac75bd3e38166c8ecc5a7f21f6b776c |
| statistics/ |