structural-variant calling with sniffles
meta:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
input:file
A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input
*.{bam,cram,snf,tsv}
index:file
Index of BAM/CAM file
*.{bai,crai}
meta2:map
Groovy Map containing reference information e.g. [ id:‘fasta’ ]
fasta:file
Reference database in FASTA format
meta3:map
Groovy Map containing tandem repeat information e.g. [ id:‘hg38’ ]
tandem_file:file
Tandem repeat file
*.bed
vcf_output:file
VCF output file
*.vcf.gz
snf_output:file
SNF output file
vcf
*.vcf.gz:file
Compressed VCF file
tbi
*.vcf.gz.tbi:file
Compressed VCF file index
*.tbi
snf
*.snf:file
SNF file
*.snf
versions
versions.yml:file
File containing software versions
versions.yml
a fast structural variant caller for long-read sequencing
