Call structural variants
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
*.{bam,cram}
input_index
Index of the BAM/CRAM file
*.{bai,crai}
vcf
A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped
*.{vcf.gz,bcf}
vcf_index
The index of the BCF/VCF file
*.{tbi,csi}
exclude_bed
An optional bed file containing regions to exclude from the called VCF
*.bed
meta2
Groovy Map containing fasta information e.g. [ id:‘test’, single_end:false ]
fasta
The reference fasta file
*.{fasta,fa}
meta3
Groovy Map containing fasta index information e.g. [ id:‘test’, single_end:false ]
fai
Index of reference fasta file to identify split-reads
*.fai
suffix
:string
A flag to specify whether the output should be in BCF or VCF format
bcf
*.{bcf,vcf.gz}
Called variants in BCF/VCF format. Set suffix to either “bcf” or “vcf” to define the output type
csi
*.{csi,tbi}
A generated csi index that matches the bcf output (not generated for vcf files)
*.{bcf.csi}
versions_delly
${task.process}
The name of the process
delly
The name of the tool
delly --version |& sed -n '1s/Delly version: *v//p'
:eval
The expression to obtain the version of the tool
versions
Structural variant discovery by integrated paired-end and split-read analysis
