bam_tumor_normal_somatic_variant_calling_gatk

Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode. f1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors. Run the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.

gatk4mutect2learnreadorientationmodelgetpileupsummariescalculatecontaminationfiltermutectcallsvariant_callingtumor_onlyfiltered_vcf

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

Description

Input

name:type

description

pattern

`ch_input`

The tumor and normal BAM files, in that order, also able to take CRAM as an input
Can contain an optional list of sample headers contained in the normal sample input file.
Structure: [ val(meta), path(input), path(input_index), val(which_norm) ]

`ch_fasta`

The reference fasta file
Structure: [ path(fasta) ]

`ch_fai`

Index of reference fasta file
Structure: [ path(fai) ]

`ch_dict`

GATK sequence dictionary
Structure: [ path(dict) ]

`ch_germline_resource`

Population vcf of germline sequencing, containing allele fractions.
Structure: [ path(germline_resources) ]

`ch_germline_resource_tbi`

Index file for the germline resource.
Structure: [ path(germline_resources_tbi) ]

`ch_panel_of_normals`

Vcf file to be used as a panel of normals.
Structure: [ path(panel_of_normals) ]

`ch_panel_of_normals_tbi`

Index for the panel of normals.
Structure: [ path(panel_of_normals_tbi) ]

`ch_interval_file`

File containing intervals.
Structure: [ path(interval_files) ]

Output

name:type

description

pattern

`versions`

Files containing software versions
Structure: [ path(versions.yml) ]

`mutect2_vcf`

Compressed vcf file to be used for variant_calling.
Structure: [ val(meta), path(vcf) ]

`mutect2_tbi`

Indexes of the mutect2_vcf file
Structure: [ val(meta), path(tbi) ]

`mutect2_stats`

Stats files for the mutect2 vcf
Structure: [ val(meta), path(stats) ]

`mutect2_f1r2`

File containing information to be passed to LearnReadOrientationModel.
Structure: [ val(meta), path(f1r2) ]

`artifact_priors`

File containing artifact-priors to be used by filtermutectcalls.
Structure: [ val(meta), path(artifact_priors) ]

`pileup_table_tumor`

File containing the tumor pileup summary table, kept separate as calculatecontamination needs them individually specified.
Structure: [ val(meta), path(table) ]

`pileup_table_normal`

File containing the normal pileup summary table, kept separate as calculatecontamination needs them individually specified.
Structure: [ val(meta), path(table) ]

`contamination_table`

File containing the contamination table.
Structure: [ val(meta), path(table) ]

`segmentation_table`

Output table containing segmentation of tumor minor allele fractions.
Structure: [ val(meta), path(table) ]

`filtered_vcf`

File containing filtered mutect2 calls.
Structure: [ val(meta), path(vcf) ]

`filtered_tbi`

Tbi file that pairs with filtered vcf.
Structure: [ val(meta), path(tbi) ]

`filtered_stats`

File containing statistics of the filtermutectcalls run.
Structure: [ val(meta), path(stats) ]