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• fixedQueries.yml

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benchmark.data.hsapiens.fixedQueries.yml Maven / Gradle / Ivy

---
baseQuery :
  study : platinum
  includeFormat : all
  includeSample : NA12877
  includeStudy :  platinum
  includeFile : platinum-genomes-vcf-NA12877_S1.genome.vcf.gz

queries :
- id : "TwoFiltersAndOneFile"
  description : ""
  query :
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"
    filter : "LowGQX;LowMQ"
  tolerationThreshold : 1500

- id : "MultipleFiltersAndTwoFiles"
  description : ""
  query :
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"
    filter : "LowGQX;LowMQ;LowQD"
  tolerationThreshold : 1500

- id : "FileAndFilter-PASS"
  description : ""
  query :
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"
    filter : "PASS"
  tolerationThreshold : 1500

- id : "SixFilters"
  description : ""
  query :
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"
    filter : "LowGQX,LowMQ,LowQD,LowGQX,LowQD,SiteConflict"
  tolerationThreshold : 1500

- id : "MultipleIncludeFilesAndSamples"
  description : ""
  query :
    release : 1
    includeSample : "NA12877,NA12878,NA12879,NA12880,NA12881,NA12882,NA12883,NA12884"
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz,platinum-genomes-vcf-NA12879_S1.genome.vcf.gz,platinum-genomes-vcf-NA12880_S1.genome.vcf.gz,platinum-genomes-vcf-NA12881_S1.genome.vcf.gz,platinum-genomes-vcf-NA12882_S1.genome.vcf.gz,platinum-genomes-vcf-NA12883_S1.genome.vcf.gz,platinum-genomes-vcf-NA12884_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "EmptyQuery"
  description : ""
  query :
    includeStudy : ""
    includeSample : ""
    includeFile : ""
  tolerationThreshold : 1500

- id : "AllIncludeStudySampleAndFile"
  description : ""
  query :
    includeStudy : all
    includeSample : all
    includeFile : all
  tolerationThreshold : 1500

- id : "TwoFiles"
  description : ""
  query :
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12882_S1.genome.vcf.gz"
    includeSample : "NA12877,NA12882"
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12882_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "FileAndSample"
  description : ""
  query :
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"
    sample : "NA12877"
  tolerationThreshold : 1500

- id : "FileAndIncludeAllStudiesOneSample"
  description : ""
  query :
    includeStudy : all
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"
    includeSample : "NA12877"
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "Info_DP_HaplotypeScore"
  description : ""
  query :
    includeSample : "NA12877,NA12878"
    info : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz:HaplotypeScore<10,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100"
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "SampleAndFilterAndGenotype"
  description : ""
  query :
    includeSample : "NA12877"
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz,platinum-genomes-vcf-NA12879_S1.genome.vcf.gz,platinum-genomes-vcf-NA12880_S1.genome.vcf.gz"
    filter : "LowGQX;LowMQ"
    genotype : "NA12877:0/1,1/1"
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz,platinum-genomes-vcf-NA12879_S1.genome.vcf.gz,platinum-genomes-vcf-NA12880_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "FileAndNegatedFilterAndGenotype"
  description : ""
  query :
    includeSample : "NA12877"
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz,platinum-genomes-vcf-NA12879_S1.genome.vcf.gz,platinum-genomes-vcf-NA12880_S1.genome.vcf.gz"
    filter : "LowGQX;LowMQ;!SiteConflict"
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz,platinum-genomes-vcf-NA12879_S1.genome.vcf.gz,platinum-genomes-vcf-NA12880_S1.genome.vcf.gz"
    genotype : "NA12877:0/1,1/1"
  tolerationThreshold : 1500

- id : "FilesFiltersAndGenotype"
  description : ""
  query :
    includeSample : "NA12877"
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz,platinum-genomes-vcf-NA12879_S1.genome.vcf.gz,platinum-genomes-vcf-NA12880_S1.genome.vcf.gz"
    genotype : "NA12877:0/1,1/1"
  tolerationThreshold : 1500

- id : "IncludeNone"
  description : ""
  query :
    includeSample : "none"
    includeFile : "none"
    includeStudy : "none"
  tolerationThreshold : 1500

- id : "Qual>50"
  description : ""
  query :
    qual : ">50"
  tolerationThreshold : 1500

- id : "Qual<50"
  description : ""
  query :
    qual : "<50"
  tolerationThreshold : 1500

- id : "Qual<<5"
  description : ""
  query :
    qual : "<<5"
  tolerationThreshold : 1500

- id : "QualAndFiltersAndFile"
  description : ""
  query :
    qual : "<50"
    filter : "LowGQX,LowMQ"
    file : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "Genotype-NA12877:1/1"
  description : ""
  query :
    includeSample : "NA12877"
    genotype : "NA12877:1/1"
  tolerationThreshold : 1500

- id : "Genotype-NA12877:0/1"
  description : ""
  query :
    includeSample : "NA12877"
    genotype : "NA12877:0/1"
  tolerationThreshold : 1500

- id : "Genotype-NA12877:HOM_REF"
  description : ""
  query :
    includeSample : "NA12877"
    genotype : "NA12877:HOM_ALT"
  tolerationThreshold : 1500

- id : "MultipleGenotype"
  description : ""
  query :
    genotype : "NA12877:0/1,1/1,NA12878:0/1,1/1"
    includeSample : "NA12877,NA12878"
    includeFile : "platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"
  tolerationThreshold : 1500

- id : "Gene-DDX11L1"
  description : ""
  query :
    gene : "DDX11L1"
  tolerationThreshold : 1500

- id : "TwoGenes"
  description : ""
  query :
    gene : "DDX11L1,WASH7P"
  tolerationThreshold : 1500

- id : "ThreeGenes"
  description : ""
  query :
    gene : "DDX11L1,WASH7P,CDH13"
  tolerationThreshold : 1500

- id : "ThreeGenesAndFourCT"
  description : ""
  query :
    gene : "DDX11L1,WASH7P,CTNNA3"
    ct : "missense_variant,start_lost,stop_lost,frameshift_variant"
  tolerationThreshold : 1500

- id : "ThreeGeneAndLOF"
  description : ""
  query :
    gene : "DDX11L1,WASH7P,CTNNA3"
    ct : "frameshift_variant,inframe_deletion,inframe_insertion,start_lost,stop_gained,stop_lost,splice_acceptor_variant,splice_donor_variant,transcript_ablation,transcript_amplification"
  tolerationThreshold : 1500

- id : "Biotype"
  description : ""
  query :
    biotype : "protein_coding"
  tolerationThreshold : 1500

- id : "PopulationFrequencyMaf"
  description : ""
  query :
    populationFrequencyMaf : "GNOMAD_GENOMES:ALL<0.01"
  tolerationThreshold : 1500

- id : "ProteinSubstitution"
  description : ""
  query :
    proteinSubstitution : "polyphen>0.1,sift=tolerant"
  tolerationThreshold : 1500

- id : "BiotypeAndLOFAndPFMAF"
  description : ""
  query :
    biotype : "protein_coding"
    ct : "frameshift_variant,inframe_deletion,inframe_insertion,start_lost,stop_gained,stop_lost,splice_acceptor_variant,splice_donor_variant,transcript_ablation,transcript_amplification"
    populationFrequencyMaf : "GNOMAD_GENOMES:ALL<0.01;1kG_phase3:ALL<0.01"
  tolerationThreshold : 1500