Given baseline and comparison sets of variants, calculate the recall/precision/f-measure
meta
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
vcf
Input SV VCF file
*.vcf.gz
tbi
Input SV VCF index file
*.vcf.gz.tbi
truth_vcf
Input VCF file with truth SVs
Input VCF index file with truth SVs
bed
BED file containing regions to compare
*.bed
meta2
Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]
fasta
Reference FASTA file
*.{fasta,fa,fna}
meta3
Groovy Map containing fasta index information e.g. [ id:'test', single_end:false ]
fai
Reference FASTA index file
*.fai
versions
File containing software versions
versions.yml
fn_vcf
VCF file with false negatives
*.fn.vcf.gz
fn_tbi
VCF index file with false negatives
*.fn.vcf.gz.tbi
fp_vcf
VCF file with false positives
*.fp.vcf.gz
fp_tbi
VCF index file with false positives
*.fp.vcf.gz.tbi
tp_base_vcf
VCF file with base true positives
*.tp-base.vcf.gz
tp_base_tbi
VCF index file with base true positives
*.tp-base.vcf.gz.tbi
tp_comp_vcf
VCF file with compared true positives
*.tp-comp.vcf.gz
tp_comp_tbi
VCF index file with compared true positives
*.tp-comp.vcf.gz.tbi
summary
Summary JSON file with results from the benchmark
*.summary.json
Structural variant comparison tool for VCFs
