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`

One or more BAM/CRAM files with their index/indices.

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

`ch_fasta`

Reference fasta file.

Structure: [ val(meta), path(fasta) ]

`ch_fai`

Reference fasta file index, and the gzip index when the reference is compressed.

Structure: [ val(meta), path(fai), path(gzi) ]

`ch_dict`

GATK sequence dictionary.

Structure: [ val(meta), path(dict) ]

`val_pon_norm`

Name given to the panel of normals, used as the sample id of the genomicsdb
workspace and of the resulting panel of normals.

`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

`genomicsdb`

Directory containing the files that compose the genomicsdb workspace.

Structure: [ val(meta), path(genomicsdb) ]

path/name_of_workspace

`mutect2_index`

Index of the mutect2 vcf file.

Structure: [ val(meta), path(tbi) ]

*.vcf.gz.tbi

`mutect2_stats`

Stats file that pairs with the mutect2 vcf file.

Structure: [ val(meta), path(stats) ]

*.vcf.gz.stats

`mutect2_vcf`

Compressed vcf file used to make the gendb workspace.

Structure: [ val(meta), path(vcf) ]

*.vcf.gz

`pon_index`

Index of the panel of normals vcf file.