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Feat/clin 2947 add exomiser #25
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@@ -1,3 +1,4 @@ | ||
familyId,sample,sequencingType,gvcf | ||
Family1,Test1,WES,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz | ||
Family1,Test2,WGS,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz | ||
familyId,sample,sequencingType,gvcf,familyPheno | ||
amily1,Test1,WES,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz,assets/exomiser/pheno/family1.yml | ||
Family1,Test2,WES,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz,assets/exomiser/pheno/family1.yml | ||
Family2,Test1,WGS,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz,assets/exomiser/pheno/family2.yml |
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## Exomiser Analysis Template. | ||
# These are all the possible options for running exomiser. Use this as a template for | ||
# your own set-up. | ||
--- | ||
analysisMode: PASS_ONLY | ||
inheritanceModes: { | ||
AUTOSOMAL_DOMINANT: 0.1, | ||
AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, | ||
AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, | ||
X_DOMINANT: 0.1, | ||
X_RECESSIVE_HOM_ALT: 0.1, | ||
X_RECESSIVE_COMP_HET: 2.0, | ||
MITOCHONDRIAL: 0.2 | ||
} | ||
frequencySources: [ | ||
UK10K, | ||
|
||
GNOMAD_E_AFR, | ||
GNOMAD_E_AMR, | ||
# GNOMAD_E_ASJ, | ||
GNOMAD_E_EAS, | ||
# GNOMAD_E_FIN, | ||
GNOMAD_E_NFE, | ||
# GNOMAD_E_OTH, | ||
GNOMAD_E_SAS, | ||
|
||
GNOMAD_G_AFR, | ||
GNOMAD_G_AMR, | ||
# GNOMAD_G_ASJ, | ||
GNOMAD_G_EAS, | ||
# GNOMAD_G_FIN, | ||
GNOMAD_G_NFE, | ||
# GNOMAD_G_OTH, | ||
GNOMAD_G_SAS | ||
] | ||
# Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM, SPLICE_AI, ALPHA_MISSENSE | ||
# REMM is trained on non-coding regulatory regions | ||
# *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files | ||
# and updated their location in the application.properties. Exomiser will not run without this. | ||
pathogenicitySources: [ REVEL, MVP ] | ||
#this is the standard exomiser order. | ||
steps: [ | ||
failedVariantFilter: { }, | ||
variantEffectFilter: { | ||
remove: [ | ||
FIVE_PRIME_UTR_EXON_VARIANT, | ||
FIVE_PRIME_UTR_INTRON_VARIANT, | ||
THREE_PRIME_UTR_EXON_VARIANT, | ||
THREE_PRIME_UTR_INTRON_VARIANT, | ||
NON_CODING_TRANSCRIPT_EXON_VARIANT, | ||
NON_CODING_TRANSCRIPT_INTRON_VARIANT, | ||
CODING_TRANSCRIPT_INTRON_VARIANT, | ||
UPSTREAM_GENE_VARIANT, | ||
DOWNSTREAM_GENE_VARIANT, | ||
INTERGENIC_VARIANT, | ||
REGULATORY_REGION_VARIANT | ||
] | ||
}, | ||
frequencyFilter: { maxFrequency: 2.0 }, | ||
pathogenicityFilter: { keepNonPathogenic: true }, | ||
inheritanceFilter: { }, | ||
omimPrioritiser: { }, | ||
hiPhivePrioritiser: { } | ||
] |
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## Exomiser genome analysis template. | ||
# These are all the possible options for running exomiser. Use this as a template for | ||
# your own set-up. | ||
--- | ||
analysisMode: PASS_ONLY | ||
inheritanceModes: { | ||
AUTOSOMAL_DOMINANT: 0.1, | ||
AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, | ||
AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, | ||
X_DOMINANT: 0.1, | ||
X_RECESSIVE_HOM_ALT: 0.1, | ||
X_RECESSIVE_COMP_HET: 2.0, | ||
MITOCHONDRIAL: 0.2 | ||
} | ||
frequencySources: [ | ||
UK10K, | ||
|
||
GNOMAD_E_AFR, | ||
GNOMAD_E_AMR, | ||
# GNOMAD_E_ASJ, | ||
GNOMAD_E_EAS, | ||
# GNOMAD_E_FIN, | ||
GNOMAD_E_NFE, | ||
# GNOMAD_E_OTH, | ||
GNOMAD_E_SAS, | ||
|
||
GNOMAD_G_AFR, | ||
GNOMAD_G_AMR, | ||
# GNOMAD_G_ASJ, | ||
GNOMAD_G_EAS, | ||
# GNOMAD_G_FIN, | ||
GNOMAD_G_NFE, | ||
# GNOMAD_G_OTH, | ||
GNOMAD_G_SAS | ||
] | ||
# Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM, SPLICE_AI, ALPHA_MISSENSE | ||
# REMM is trained on non-coding regulatory regions | ||
# *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files | ||
# and updated their location in the application.properties. Exomiser will not run without this. | ||
pathogenicitySources: [ REVEL, MVP ] | ||
# this is the recommended order for a genome-sized analysis. | ||
steps: [ | ||
hiPhivePrioritiser: { }, | ||
# running the prioritiser followed by a priorityScoreFilter will remove genes | ||
# which are least likely to contribute to the phenotype defined in hpoIds, this will | ||
# dramatically reduce the time and memory required to analyse a genome. | ||
# 0.501 is a good compromise to select good phenotype matches and the best protein-protein interactions hits from hiPhive | ||
priorityScoreFilter: { priorityType: HIPHIVE_PRIORITY, minPriorityScore: 0.501 }, | ||
failedVariantFilter: { }, | ||
regulatoryFeatureFilter: { }, | ||
frequencyFilter: { maxFrequency: 2.0 }, | ||
pathogenicityFilter: { keepNonPathogenic: true }, | ||
inheritanceFilter: { }, | ||
omimPrioritiser: { } | ||
] |
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--- | ||
id: family1 | ||
proband: | ||
subject: | ||
id: testN | ||
sex: FEMALE | ||
phenotypicFeatures: | ||
- type: | ||
id: HP:0001159 | ||
label: Syndactyly | ||
|
||
pedigree: | ||
persons: | ||
- individualId: testN | ||
paternalId: testT | ||
sex: FEMALE | ||
affectedStatus: AFFECTED | ||
- individualId: testT | ||
sex: MALE | ||
affectedStatus: UNAFFECTED | ||
|
||
metaData: | ||
resources: | ||
- id: hp | ||
name: human phenotype ontology | ||
url: http://purl.obolibrary.org/obo/hp.owl | ||
version: hp/releases/2019-11-08 | ||
namespacePrefix: HP | ||
iriPrefix: 'http://purl.obolibrary.org/obo/HP_' | ||
phenopacketSchemaVersion: 2.0 |
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Remove last parenthesis + update link
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Done