Nextflow Registry | nf-core/gatk4/concordance@0.0.0-6c4ed3a

nf-core/gatk4/concordance @ 0.0.0-6c4ed3a

Evaluate concordance of an input VCF against a validated truth VCF

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @kubranarci

Maintainers: @kubranarci

Evaluate concordance of an input VCF against a validated truth VCF

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

include { GATK4_CONCORDANCE } from 'nf-core/gatk4/concordance'

MIT License

Process

`Name`	`GATK4_CONCORDANCE`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	Evaluation VCF file created with a variant caller `*.vcf.gz`
`vcf_tbi` file	Index file for the evaluation VCF `*.vcf.gz.tbi`
`truth` file	Truth VCF file created with a variant caller `*.vcf.gz`
`truth_tbi` file	Index file for the truth VCF `*.vcf.gz.tbi`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'bed' ]`
`intervals` file	Bed file with the genomic regions included in the library (optional) `*.bed`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'fasta' ]`
`fasta` file	Reference FASTA file `*.{fasta,fa}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'fai' ]`
`fai` file	Index of the reference FASTA file `*.fai`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. `[ id:'dict' ]`
`dict` file	Sequence dictionary of the reference FASTA file `*.dict`

Output 4 channels

#1 tpfn tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.tpfn.vcf` file	Eval VCF file with tagged with TP or FN in "INFO/STATUS" `*.vcf`

#2 tpfp tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.tpfp.vcf` file	Eval VCF file with tagged with TP or FP in "INFO/STATUS" `*.vcf`

#3 summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.tsv` file	A tab-delimited file containing the metrics with number of TPs, FPs, FNs, Precision, Recall and F1 statistics `*.tsv`

#4 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gatk4	Genome Analysis Toolkit (GATK4)	https://gatk.broadinstitute.org/hc/en-us