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50 lines
1.6 KiB
YAML
Executable file
50 lines
1.6 KiB
YAML
Executable file
name: sequenzautils_bam2seqz
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description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
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keywords:
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- bam2seqz
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tools:
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- sequenzautils:
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description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
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homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html
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documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html
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doi: 10.1093/annonc/mdu479
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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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- normalbam:
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type: file
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description: BAM file from the reference/normal sample
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pattern: "*.{bam}"
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- tumourbam:
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type: file
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description: BAM file from the tumour sample
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: Reference FASTA file
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pattern: "*.{fasta}"
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- wigfile:
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type: file
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description: GC content wiggle file
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pattern: "*.{wig.gz}"
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- seqz:
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type: file
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description: Seqz file
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pattern: "*.{seqz.gz}"
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authors:
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- "@kaurravneet4123"
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