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meta.yml
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meta.yml
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name: gatk4_haplotypecaller
description: Call germline SNPs and indels via local re-assembly of haplotypes
keywords:
- gatk4
- haplotypecaller
- haplotype
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- dbsnp:
type: file
description: VCF file containing known sites (optional)
- dbsnp_tbi:
type: file
description: VCF index of dbsnp (optional)
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf:
type: file
description: Compressed VCF file
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of VCF file
pattern: "*.vcf.gz.tbi"
authors:
- "@suzannejin"
- "@FriederikeHanssen"