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