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74 lines
2.1 KiB
YAML
74 lines
2.1 KiB
YAML
name: "gatk4_reblockgvcf"
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description: Condenses homRef blocks in a single-sample GVCF
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keywords:
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- gatk4
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- reblockgvcf
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- gvcf
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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', single_end:false ]
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- gvcf:
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type: file
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description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode
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pattern: "*.{vcf,gvcf}.gz"
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- tbi:
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type: file
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description: Index of the GVCF file
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pattern: "*.tbi"
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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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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- dbsnp:
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type: file
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description: VCF file containing known sites (optional)
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- dbsnp_tbi:
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type: file
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description: VCF index of dbsnp (optional)
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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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- gvcf:
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type: file
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description: Filtered GVCF
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pattern: "*rb.g.vcf.gz"
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- tbi:
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type: file
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description: Index of the filtered GVCF
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pattern: "*rb.g.vcf.gz.tbi"
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authors:
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- "@nvnieuwk"
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