Call structural variants
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
*.{bam,cram}
input_index{:bash}
Index of the BAM/CRAM file
*.{bai,crai}
vcf{:bash}
A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped
*.{vcf.gz,bcf}
vcf_index{:bash}
The index of the BCF/VCF file
*.{tbi,csi}
exclude_bed{:bash}
An optional bed file containing regions to exclude from the called VCF
*.bed
meta2{:bash}
Groovy Map containing fasta information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
The reference fasta file
*.{fasta,fa}
meta3{:bash}
Groovy Map containing fasta index information e.g. [ id:‘test’, single_end:false ]
fai{:bash}
Index of reference fasta file to identify split-reads
*.fai
bcf{:bash}
*.{bcf,vcf.gz}{:bash}
Called variants in BCF/VCF format. Specify either “bcf” or “vcf” in ext.suffix to define the output type
*.{bcf,vcf.gz}
csi{:bash}
*.{csi,tbi}{:bash}
A generated csi index that matches the bcf output (not generated for vcf files)
*.{bcf.csi}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Structural variant discovery by integrated paired-end and split-read analysis
