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79 lines
2.8 KiB
YAML
79 lines
2.8 KiB
YAML
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name: gatk4_variantrecalibrator
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description: |
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Build a recalibration model to score variant quality for filtering purposes.
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It is highly recommended to follow GATK best practices when using this module,
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the gaussian mixture model requires a large number of samples to be used for the
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tool to produce optimal results. For example, 30 samples for exome data. For more details see
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https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-
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keywords:
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- VariantRecalibrator
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- gatk4
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- recalibration_model
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- vcf:
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type: file
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description: input vcf file containing the variants to be recalibrated
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: tbi file matching with -vcf
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pattern: "*.vcf.gz.tbi"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- resvcfs:
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type: list
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description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command.
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pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz'
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- restbis:
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type: list
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description: tbis for the corresponding vcfs files to be used as truth, training and known resources.
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pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi'
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output:
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- recal:
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type: file
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description: Output recal file used by ApplyVQSR
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pattern: "*.recal"
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- idx:
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type: file
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description: Index file for the recal output file
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pattern: "*.idx"
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- tranches:
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type: file
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description: Output tranches file used by ApplyVQSR
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pattern: "*.tranches"
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- plots:
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type: file
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description: Optional output rscript file to aid in visualization of the input data and learned model.
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pattern: "*plots.R"
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- version:
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type: file
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description: File containing software versions
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pattern: "*.versions.yml"
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authors:
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- "@GCJMackenzie"
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