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71 lines
2 KiB
YAML
71 lines
2 KiB
YAML
name: "gatk_indelrealigner"
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description: Performs local realignment around indels to correct for mapping errors
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keywords:
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- bam
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- vcf
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- variant calling
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- indel
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- realignment
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tools:
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- "gatk":
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description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
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homepage: "https://gatk.broadinstitute.org/hc/en-us"
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documentation: "https://github.com/broadinstitute/gatk-docs"
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licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
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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', single_end:false ]
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- input:
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type: file
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description: Sorted and indexed BAM/CRAM/SAM file
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pattern: "*.bam"
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- index:
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type: file
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description: BAM index file
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pattern: "*.bai"
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- intervals:
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type: file
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description: Intervals file created by gatk3 RealignerTargetCreator
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pattern: "*.{intervals,list}"
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- fasta:
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type: file
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description: Reference file used to generate BAM file
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pattern: ".{fasta,fa,fna}"
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- fai:
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type: file
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description: Index of reference file used to generate BAM file
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pattern: ".fai"
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- dict:
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type: file
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description: GATK dict file for reference
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pattern: ".dict"
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- known_vcf:
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type: file
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description: Optional input VCF file(s) with known indels
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pattern: ".vcf"
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output:
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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', single_end:false ]
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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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- bam:
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type: file
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description: Sorted and indexed BAM/CRAM/SAM file with local realignment around variants
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pattern: "*.bam"
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- bai:
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type: file
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description: Output BAM Index file
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pattern: "*.bai"
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authors:
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- "@jfy133"
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