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73 lines
2 KiB
YAML
73 lines
2 KiB
YAML
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name: "angsd_docounts"
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description: Calculates base frequency statistics across reference positions from BAM.
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keywords:
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- angsd
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- population genetics
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- allele counts
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- doCounts
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tools:
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- "angsd":
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description: "ANGSD: Analysis of next generation Sequencing Data"
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homepage: "http://www.popgen.dk/angsd/"
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documentation: "http://www.popgen.dk/angsd/"
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tool_dev_url: "https://github.com/ANGSD/angsd"
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doi: "10.1186/s12859-014-0356-4"
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licence: "['GPL v3, 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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- bam:
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type: file
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description: A list of BAM or CRAM files
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pattern: "*.{bam,cram}"
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- bai:
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type: file
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description: List of BAM/CRAM index files
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pattern: "*.{bai,csi}"
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- minqfile:
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type: file
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description: File with individual quality score thresholds
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pattern: "*"
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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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- depth_sample:
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type: file
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description: Distribution of sequencing depths
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pattern: "*.depthSample"
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- depth_global:
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type: file
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description: Distribution of sequencing depths
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pattern: "*.depthGlobal"
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- qs:
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type: file
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description: Distribution of scores
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pattern: "*.qs"
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- pos:
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type: file
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description: Various types of depth statistics (depending on value for -dumpCounts)
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pattern: "*.pos.gz"
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- counts:
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type: file
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description: Various types of statistics (related to pos.gz)
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pattern: "*.counts.gz"
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- icounts:
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type: file
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description: Internal format for dumping binary single chrs. Useful for ANGSD contamination
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pattern: "*.icnts.gz"
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authors:
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- "@jfy133"
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