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Add fractionCoverage20x #124

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Jan 11, 2024
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Add fractionCoverage20x #124

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04a0787
Add fractionCoverage20x to CohortAlleleFrequency schema and examples
theferrit32 Jan 11, 2024
f7dd7d6
Add description to meanDepth. Minor formatting.
theferrit32 Jan 11, 2024
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5 changes: 3 additions & 2 deletions docs/Modeling/CohortFrequency/simple_result_example.json
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@
"popFreqId": "1-55051215-G-GA.AFR"
},
"homozygotes": 9,
"meanDepth": 32.8
"meanDepth": 32.8,
"fractionCoverage20x": 0.9754
},
"subcohortFrequency": [
{
Expand Down Expand Up @@ -143,4 +144,4 @@
}
}
]
}
}
1 change: 1 addition & 0 deletions docs/Modeling/CohortFrequency/simple_result_example.yaml
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Expand Up @@ -38,6 +38,7 @@ ancillaryResults:
homozygotes: 9 # Number of Homozygotes
qualityMeasures:
meanDepth: 32.8 # Mean depth of coverage
fractionCoverage20x: 0.9754 # Fraction of individuals with at least 20x coverage
subcohortFrequency:
- id: 1-55051215-G-GA.AFR
type: CohortAlleleFrequency
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13 changes: 9 additions & 4 deletions schema/cohortAlleleFreq.json
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Expand Up @@ -361,6 +361,11 @@
"type": "object",
"properties": {
"meanDepth": {
"description": "The mean depth of coverage.",
"type": "number"
},
"fractionCoverage20x": {
"description": "The fraction of individuals with at least 20x coverage.",
"type": "number"
},
"qcFilters": {
Expand All @@ -374,19 +379,19 @@
"type": "boolean"
},
"lowComplexityRegion": {
"description": "This flag indicates the variant is found in a low complexity region. These regions were identified with the symmetric DUST algorithm at a score threshold of 30.",
"description": "This flag indicates the variant is found in a low complexity region. These regions were identified with the symmetric DUST algorithm at a score threshold of 30.",
"type": "boolean"
},
"lowConfidenceLossOfFunctionError": {
"description": "Low confidence in predicted Loss of Function (pLoF), where variant is determined by LOFTEE to be unlikely loss of function for a transcript.",
"description": "Low confidence in predicted Loss of Function (pLoF), where variant is determined by LOFTEE to be unlikely loss of function for a transcript.",
"type": "boolean"
},
"lossOfFunctionWarning": {
"description": "A warning provided by LOFTEE to use caution when interpreting the transcript or variant.",
"type": "boolean"
},
"noncodingTranscriptError": {
"description": "Marked in a putative loss of function category by VEP (essential splice, stop-gained, or frameshift) but appears on a non-protein-coding transcript.",
"description": "Marked in a putative loss of function category by VEP (essential splice, stop-gained, or frameshift) but appears on a non-protein-coding transcript.",
"type": "boolean"
},
"heterozygousSkewedAlleleCount": {
Expand All @@ -413,4 +418,4 @@
"cohort"
],
"additionalProperties": false
}
}
12 changes: 9 additions & 3 deletions schema/cohortAlleleFreq.yaml
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Expand Up @@ -270,6 +270,12 @@ properties:
type: object
properties:
meanDepth:
description: >-
The mean depth of coverage.
type: number
fractionCoverage20x:
description: >-
The fraction of individuals with at least 20x coverage.
type: number
qcFilters:
type: array
Expand All @@ -281,12 +287,12 @@ properties:
type: boolean
lowComplexityRegion:
description: >-
This flag indicates the variant is found in a low complexity region. These regions were identified
This flag indicates the variant is found in a low complexity region. These regions were identified
with the symmetric DUST algorithm at a score threshold of 30.
type: boolean
lowConfidenceLossOfFunctionError:
description: >-
Low confidence in predicted Loss of Function (pLoF), where variant is determined by LOFTEE
Low confidence in predicted Loss of Function (pLoF), where variant is determined by LOFTEE
to be unlikely loss of function for a transcript.
type: boolean
lossOfFunctionWarning:
Expand All @@ -295,7 +301,7 @@ properties:
type: boolean
noncodingTranscriptError:
description: >-
Marked in a putative loss of function category by VEP (essential splice, stop-gained, or frameshift)
Marked in a putative loss of function category by VEP (essential splice, stop-gained, or frameshift)
but appears on a non-protein-coding transcript.
type: boolean
heterozygousSkewedAlleleCount:
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