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* Update versions * update checksums + remove variables as input for applyvqsr * sneak in removal of values and provide them via modules.config * update another checksum * more checksums * move vairable to config * remove controlfreec, wrong branch * add line break
76 lines
2.5 KiB
YAML
76 lines
2.5 KiB
YAML
name: gatk4_applyvqsr
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description: |
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Apply a score cutoff to filter variants based on a recalibration table.
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AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).
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Specifically, it applies filtering to the input variants based on the recalibration table produced
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in the first step by VariantRecalibrator and a target sensitivity value.
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keywords:
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- gatk4
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- applyvqsr
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- VQSR
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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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licence: ['Apache-2.0']
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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: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
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pattern: "*.vcf"
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- tbi:
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type: file
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description: Tbi index for the input vcf file.
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pattern: "*.vcf.tbi"
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- recal:
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type: file
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description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
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pattern: "*.recal"
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- recalidx:
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type: file
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description: Index file for the recalibration file.
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pattern: ".recal.idx"
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- tranches:
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type: boolean
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description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
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pattern: ".tranches"
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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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output:
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- vcf:
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type: file
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description: compressed vcf file containing the recalibrated variants.
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: Index of recalibrated vcf file.
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pattern: "*vcf.gz.tbi"
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- versions:
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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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