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

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

`ch_fai`

Index of reference fasta file, 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) ]

`ch_alleles`

VCF file to be used for force calling of alleles.

Structure: [ path(alleles) ]

`ch_alleles_tbi`

Index of VCF file of alleles for force calling.

Structure: [ path(alleles_tbi) ]

`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

description

pattern

`artifact_priors`

File containing artifact-priors to be used by filtermutectcalls.

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

`contamination_table`

File containing the contamination table.

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

`filtered_stats`

File containing statistics of the filtermutectcalls run.

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

`filtered_tbi`

Tbi file that pairs with filtered vcf.

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

`filtered_vcf`

File containing filtered mutect2 calls.

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

`mutect2_f1r2`

File containing information to be passed to LearnReadOrientationModel.

Structure: [ val(meta), path(f1r2) ]

`mutect2_stats`

Stats files for the mutect2 vcf

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

`mutect2_tbi`

Indexes of the mutect2_vcf file

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

`mutect2_vcf`

Compressed vcf file to be used for variant_calling.

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

`pileup_table_normal`

File containing the normal pileup summary table, kept separate as calculatecontamination needs them individually specified.

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

`pileup_table_tumor`

File containing the tumor pileup summary table, kept separate as calculatecontamination needs them individually specified.

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

`segmentation_table`

Output table containing segmentation of tumor minor allele fractions.

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

bam_tumor_normal_somatic_variant_calling_gatk

Description

Input

`ch_input`

`ch_fasta`

`ch_fai`

`ch_dict`

`ch_alleles`

`ch_alleles_tbi`

`ch_germline_resource`

`ch_germline_resource_tbi`

`ch_panel_of_normals`

`ch_panel_of_normals_tbi`

`ch_interval_file`

Output

`artifact_priors`

`contamination_table`

`filtered_stats`

`filtered_tbi`

`filtered_vcf`

`mutect2_f1r2`

`mutect2_stats`

`mutect2_tbi`

`mutect2_vcf`

`pileup_table_normal`

`pileup_table_tumor`

`segmentation_table`

included modules and subworkflows

maintainer

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