type/

Call somatic SNVs and indels via local assembly of haplotypes.

gatk4haplotypeindelsmutect2snvssomatic

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/mutect2

Description

Call somatic SNVs and indels via local assembly of haplotypes.

Input

name:type

description

pattern

`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}

`meta2:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fasta:file`

The reference fasta file

*.fasta

`meta3:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fai:file`

Index of reference fasta file

*.fasta.fai

`meta4:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`dict:file`

GATK sequence dictionary

*.dict

`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

name:type

description

pattern

`vcf`

`meta:file`

compressed vcf file

*.vcf.gz

`*.vcf.gz:file`

compressed vcf file

*.vcf.gz

`tbi`

`meta:file`

Index of vcf file

*vcf.gz.tbi

`*.tbi:file`

Index of vcf file

*vcf.gz.tbi

`stats`

`meta:file`

Stats file that pairs with output vcf file

*vcf.gz.stats

`*.stats:file`

Stats file that pairs with output vcf file

*vcf.gz.stats

`f1r2`

`meta:file`

file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)

*.f1r2.tar.gz

`*.f1r2.tar.gz:file`

file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)

*.f1r2.tar.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590

type/

Description

Input

`meta:map`

`input:list`

`input_index:list`

`intervals:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fai:file`

`meta4:map`

`dict:file`

`germline_resource:file`

`germline_resource_tbi:file`

`panel_of_normals:file`

`panel_of_normals_tbi:file`

Output

`vcf`

`meta:file`

`*.vcf.gz:file`

`tbi`

`meta:file`

`*.tbi:file`

`stats`

`meta:file`

`*.stats:file`

`f1r2`

`meta:file`

`*.f1r2.tar.gz:file`

`versions`

`versions.yml:file`

Tools

gatk4
Apache-2.0

included in

maintainers

get in touch

type/

Description

Input

meta:map

input:list

input_index:list

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

germline_resource:file

germline_resource_tbi:file

panel_of_normals:file

panel_of_normals_tbi:file

Output

vcf

meta:file

*.vcf.gz:file

tbi

meta:file

*.tbi:file

stats

meta:file

*.stats:file

f1r2

meta:file

*.f1r2.tar.gz:file

versions

versions.yml:file

Tools

gatk4 Apache-2.0

included in

maintainers

get in touch

`meta:map`

`input:list`

`input_index:list`

`intervals:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fai:file`

`meta4:map`

`dict:file`

`germline_resource:file`

`germline_resource_tbi:file`

`panel_of_normals:file`

`panel_of_normals_tbi:file`

`vcf`

`meta:file`

`*.vcf.gz:file`

`tbi`

`meta:file`

`*.tbi:file`

`stats`

`meta:file`

`*.stats:file`

`f1r2`

`meta:file`

`*.f1r2.tar.gz:file`

`versions`

`versions.yml:file`

gatk4
Apache-2.0