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79a9d5e1ea
NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
64 lines
1.9 KiB
YAML
64 lines
1.9 KiB
YAML
name: ngscheckmate_ncm
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description: Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.
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keywords:
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- ngscheckmate
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- matching
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- snp
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tools:
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- ngscheckmate:
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description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
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homepage: https://github.com/parklab/NGSCheckMate
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documentation: https://github.com/parklab/NGSCheckMate
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tool_dev_url: https://github.com/parklab/NGSCheckMate
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doi: "doi:/10.1093/nar/gkx193"
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licence: ['MIT']
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input:
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- files:
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type: file
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description: VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too.
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pattern: "*.{vcf,vcf.gz,bam,bai}"
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- snp_bed:
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type: file
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description: BED file containing the SNPs to analyse
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pattern: "*.{bed}"
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- fasta:
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type: file
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description: fasta file for the genome, only used in the bam mode
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pattern: "*.{bed}"
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output:
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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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- pdf:
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type: file
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description: A pdf containing a dendrogram showing how the samples match up
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pattern: "*.{pdf}"
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- corr_matrix:
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type: file
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description: A text file containing the correlation matrix between each sample
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pattern: "*corr_matrix.txt"
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- matched:
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type: file
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description: A txt file containing only the samples that match with each other
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pattern: "*matched.txt"
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- all:
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type: file
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description: A txt file containing all the sample comparisons, whether they match or not
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pattern: "*all.txt"
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- vcfs:
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type: file
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description: If ran in bam mode, vcf files for each sample giving the SNP calls
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pattern: "*.vcf"
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authors:
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- "@sppearce"
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