Description

Genotype structural variants using paragraph and grmpy

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

variants:file

A VCF or JSON file containing called structural variants

*.{vcf,json}

variants_index:file

The index for the VCF file

*.tbi

reads:file

BAM or CRAM file(s) to genotype against. These should be specified inside the manifest

*.{bam,cram}

reads_index:file

The index/indices for the BAM/CRAM file(s)

*.{bai,crai}

manifest:file

A tab separated file containing information on the BAM/CRAM files. This information can be generated using paragraph/idxdepth. More information can be found here: https://github.com/Illumina/paragraph#sample-manifest

meta2:map

Groovy Map containing sample information for the FASTA file e.g. [ id:‘test’, single_end:false ]

fasta:file

The reference FASTA file used to generate the VCF and BAM/CRAM files

*.{fa,fasta,fna}

meta3:map

Groovy Map containing sample information for the FASTA index file e.g. [ id:‘test’, single_end:false ]

fasta_fai:file

The index of the reference FASTA file

*.fai

Output

name:type
description
pattern

vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.vcf.gz:file

The genotyped VCF file in BGZIP format

*.vcf.gz

json

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.json.gz:file

The genotyped JSON file in GZIP format

*.json.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

paragraph
Apache License 2.0

Graph realignment tools for structural variants

github.com/Illumina/paragraph 10.1101/635011
maintainer
Github user nvnieuwk
get in touch
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