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56 lines
1.6 KiB
YAML
56 lines
1.6 KiB
YAML
name: gatk4_combinegvcfs
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description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
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keywords:
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- gvcf
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- gatk4
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- vcf
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- combinegvcfs
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- Short_Variant_Discovery
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tools:
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- gatk4:
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description:
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Genome Analysis Toolkit (GATK4). 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/articles/360037593911-CombineGVCFs
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tool_dev_url: https://github.com/broadinstitute/gatk
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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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- 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: FASTA index file
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pattern: "*.{fai}"
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- dict:
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type: file
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description: FASTA dictionary file
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pattern: "*.{dict}"
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- vcf:
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type: file
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description: Compressed VCF files
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pattern: "*.vcf.gz"
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- vcf_idx:
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type: file
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description: VCF Index file
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pattern: "*.{fai}"
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output:
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- gvcf:
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type: file
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description: Compressed Combined GVCF file
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pattern: "*.combined.g.vcf.gz"
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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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- "@sateeshperi"
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- "@mjcipriano"
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- "@hseabolt"
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