Nextflow Registry | nf-core/gatk4/mutect2@0.0.0-6c4ed3a

nf-core/gatk4/mutect2 @ 0.0.0-6c4ed3a

Call somatic SNVs and indels via local assembly of haplotypes.

gatk4 haplotype indels mutect2 snvs somatic

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @GCJMackenzie @ramprasadn

Maintainers: @GCJMackenzie @ramprasadn

Call somatic SNVs and indels via local assembly of haplotypes.

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

include { GATK4_MUTECT2 } from 'nf-core/gatk4/mutect2'

MIT License

Process

`Name`	`GATK4_MUTECT2`

Input 10 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`input` list	list of BAM files, also able to take CRAM as an input `*.{bam/cram}`
`input_index` list	list of BAM file indexes, also able to take CRAM indexes as an input `*.{bam.bai/cram.crai}`
`intervals` file	Specify region the tools is run on. `.{bed,interval_list}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	The reference fasta file `*.{fasta,fasta.gz}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Index of reference fasta file `*.{fasta.fai,fasta.fai.gz}`
`gzi` file	Index of bgzipped reference fasta file `*.fasta.gz.gzi`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`dict` file	GATK sequence dictionary `*.dict`

`alleles` file	vcf file to be used to force-call alleles. `*.vcf.gz`

`alleles_tbi` file	Index file for alleles to be force-called. `*.vcf.gz.tbi`

`germline_resource` file	Population vcf of germline sequencing, containing allele fractions. `*.vcf.gz`

`germline_resource_tbi` file	Index file for the germline resource. `*.vcf.gz.tbi`

`panel_of_normals` file	vcf file to be used as a panel of normals. `*.vcf.gz`

`panel_of_normals_tbi` file	Index for the panel of normals. `*.vcf.gz.tbi`

Output 5 channels

#1 tbi tuple

`meta` map	A Groovy map containing sample information
`*.tbi` file	Index of vcf file `*vcf.gz.tbi`

#2 vcf tuple

`meta` map	A Groovy map containing sample information
`*.vcf.gz` file	compressed vcf file `*.vcf.gz`

#3 f1r2 tuple

`meta` map	A Groovy map containing sample information
`*.f1r2.tar.gz` file	file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run) `*.f1r2.tar.gz`

#4 stats tuple

`meta` map	A Groovy map containing sample information
`*.stats` file	Stats file that pairs with output vcf file `*vcf.gz.stats`

#5 versions_gatk4 tuple