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71 lines
2.3 KiB
YAML
71 lines
2.3 KiB
YAML
name: gatk4_getpileupsummaries
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description: |
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Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
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keywords:
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- gatk4
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- getpileupsumaries
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- readcountssummary
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- germlinevariantsites
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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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- input:
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type: file
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description: BAM/CRAM file to be summarised.
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAM/CRAM file index.
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pattern: "*.{bai,crai}"
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- intervals:
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type: file
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description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.
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pattern: "*.interval_list"
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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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- variants:
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type: file
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description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
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pattern: "*.vcf.gz"
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- variants_tbi:
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type: file
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description: Index file for the germline resource.
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pattern: "*.vcf.gz.tbi"
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output:
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- pileup:
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type: file
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description: File containing the pileup summary table.
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pattern: "*.pileups.table"
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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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