Nextflow Registry | nf-core/rtgtools/vcfeval@0.0.0-6c4ed3a

nf-core/rtgtools/vcfeval @ 0.0.0-6c4ed3a

The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set

benchmarking vcf rtg-tools

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set

Add the following snippet to your workflow script to include this module.

include { RTGTOOLS_VCFEVAL } from 'nf-core/rtgtools/vcfeval'

MIT License

Process

`Name`	`RTGTOOLS_VCFEVAL`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`query_vcf` file	A VCF with called variants to benchmark against the standard `*.{vcf,vcf.gz}`
`query_vcf_tbi` file	The index of the VCF file with called variants to benchmark against the standard `*.{vcf.gz.tbi, vcf.tbi}`
`truth_vcf` file	A standard VCF to compare against `*.{vcf,vcf.gz}`
`truth_vcf_tbi` file	The index of the standard VCF to compare against `*.{vcf.gz.tbi, vcf.tbi}`
`truth_bed` file	A BED file containing the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) This input should be used to provide the golden truth BED files. `*.bed`
`regions_bed` file	A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) This input should be used to provide the regions used by the analysis `*.bed`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`sdf` file	The SDF (RTG Sequence Data File) folder of the reference genome

Output 14 channels

#1 fn_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fn.vcf.gz.tbi` file	The index of the VCF file for the false negative variants `*.fn.vcf.gz.tbi`

#2 fn_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fn.vcf.gz` file	A VCF file for the false negative variants `*.fn.vcf.gz`

#3 fp_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fp.vcf.gz.tbi` file	The index of the VCF file for the false positive variants `*.fp.vcf.gz.tbi`

#4 fp_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fp.vcf.gz` file	A VCF file for the false positive variants `*.fp.vcf.gz`

#5 tp_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tp.vcf.gz.tbi` file	The index of the VCF file for the true positive variants `*.tp.vcf.gz.tbi`

#6 tp_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tp.vcf.gz` file	A VCF file for the true positive variants `*.tp.vcf.gz`

#7 phasing tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.phasing.txt` file	A TXT file containing the data on the phasing `*.phasing.txt`

#8 snp_roc tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.snp_roc.tsv.gz` file	TSV files containing ROC data for the SNPs `*.snp_roc.tsv.gz`