bam_create_som_pon_gatk

Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.

gatk4mutect2genomicsdbimportcreatesomaticpanelofnormalsvariant_callinggenomicsdb_workspacepanel_of_normals

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_create_som_pon_gatk

Description

Input

name:type

description

pattern

`ch_mutect2_in :list`

An input channel containing the following files:

input: One or more BAM/CRAM files
input_index: The index/indices from the BAM/CRAM file(s)
interval_file: An interval file to be used with the mutect call
Structure: [ meta, input, input_index, interval_file ]

`fasta :file`

The reference fasta file

*.fasta

`fai :file`

Index of reference fasta file

*.fasta.fai

`dict :file`

GATK sequence dictionary

*.dict

Output

name:type

description

pattern

`versions :file`

File containing software versions

versions.yml

`mutect2_vcf :list`

List of compressed vcf files to be used to make the gendb workspace

[ *.vcf.gz ]

`mutect2_index :list`

List of indexes of mutect2_vcf files

[ *vcf.gz.tbi ]

`mutect2_stats :list`

List of stats files that pair with mutect2_vcf files

[ *vcf.gz.stats ]

`genomicsdb :directory`

Directory containing the files that compose the genomicsdb workspace.

path/name_of_workspace

`pon_vcf :file`

Panel of normal as compressed vcf file

*.vcf.gz

`pon_index :file`

Index of pon_vcf file

*vcf.gz.tbi