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58 lines
1.8 KiB
YAML
58 lines
1.8 KiB
YAML
name: "bcftools_roh"
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description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
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keywords:
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- roh
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tools:
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- "roh":
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description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered."
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homepage: https://www.htslib.org/
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documentation: http://www.htslib.org/doc/bcftools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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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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- vcf:
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type: file
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description: VCF file
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pattern: "*.{vcf,.vcf.gz}"
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- af_file:
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type: file
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description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
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- af_file_tbi:
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type: file
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description: "tbi index of af_file."
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- genetic_map:
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type: file
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description: "Genetic map in the format required also by IMPUTE2."
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- regions_file:
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type: file
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description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
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- samples_file:
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type: file
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description: "File of sample names to include or exclude if prefixed with '^'."
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- targets_file:
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type: file
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description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
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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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- roh:
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type: file
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description: Contains site-specific and/or per-region runs of homo/autozygosity calls.
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pattern: "*.{roh}"
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authors:
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- "@ramprasadn"
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