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

description

pattern

`ch_input`

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)
Structure: [ meta, path(input), path(input_index) ]

`ch_fasta`

Reference fasta file
Structure: [ meta, path(fasta) ]

`ch_fai`

Reference fasta file index
Structure: [ meta, path(fai) ]

`ch_dict`

GATK sequence dictionary
Structure: [ meta, path(dict) ]

`ch_intervals_gendb`

Interval file used for GenomicsDBImport

*.{bed,interval_list}

`ch_intervals_num`

Intervals channel for scatter and gather strategy. Each item is a tuple of
an interval file and the total number of intervals. Use [ [], 0 ] if no intervals.
Structure: [ path(intervals), val(num_intervals) ]

Output

name

description

pattern

`mutect2_vcf`

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

[ *.vcf.gz ]

`mutect2_index`

List of indexes of mutect2_vcf files

[ *vcf.gz.tbi ]

`mutect2_stats`

List of stats files that pair with mutect2_vcf files

[ *vcf.gz.stats ]

`genomicsdb`

Directory containing the files that compose the genomicsdb workspace.

path/name_of_workspace

`pon_vcf`

Panel of normal as compressed vcf file

*.vcf.gz

`pon_index`

Index of pon_vcf file

*vcf.gz.tbi