bam_tumor_only_somatic_variant_calling_gatk

Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.

gatk4mutect2getpileupsummariescalculatecontaminationfiltermutectcallsvariant_callingtumor_onlyfiltered_vcf

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

Description

Input

name:type

description

pattern

`meta :map`

Groovy Map containing sample information
e.g. [ id:‘test’ ]

`input :list`

list containing one BAM file, also able to take CRAM as an input

[ *.{bam/cram} ]

`input_index :list`

list containing one BAM file indexe, also able to take CRAM index as an input

[ *.{bam.bai/cram.crai} ]

`fasta :file`

The reference fasta file

*.fasta

`fai :file`

Index of reference fasta file

*.fasta.fai

`dict :file`

GATK sequence dictionary

*.dict

`germline_resource :file`

Population vcf of germline sequencing, containing allele fractions.

*.vcf.gz

`germline_resource_tbi :file`

Index file for the germline resource.

*.vcf.gz.tbi

`panel_of_normals :file`

vcf file to be used as a panel of normals.

*.vcf.gz

`panel_of_normals_tbi :file`

Index for the panel of normals.

*.vcf.gz.tbi

`interval_file :file`

File containing intervals.

*.interval_list

Output

name:type

description

pattern

`versions :file`

File containing software versions

versions.yml

`mutect2_vcf :file`

Compressed vcf file to be used for variant_calling.

[ *.vcf.gz ]

`mutect2_tbi :file`

Indexes of the mutect2_vcf file

[ *vcf.gz.tbi ]

`mutect2_stats :file`

Stats files for the mutect2 vcf

[ *vcf.gz.stats ]

`pileup_table :file`

File containing the pileup summary table.

*.pileups.table

`contamination_table :file`

File containing the contamination table.

*.contamination.table

`segmentation_table :file`

Output table containing segmentation of tumor minor allele fractions.

*.segmentation.table

`filtered_vcf :file`

file containing filtered mutect2 calls.

*.vcf.gz

`filtered_tbi :file`

tbi file that pairs with filtered vcf.

*.vcf.gz.tbi

`filtered_stats :file`

file containing statistics of the filtermutectcalls run.

*.filteringStats.tsv

bam_tumor_only_somatic_variant_calling_gatk

Description

Input

`meta :map`

`input :list`

`input_index :list`

`fasta :file`

`fai :file`

`dict :file`

`germline_resource :file`

`germline_resource_tbi :file`

`panel_of_normals :file`

`panel_of_normals_tbi :file`

`interval_file :file`

Output

`versions :file`

`mutect2_vcf :file`

`mutect2_tbi :file`

`mutect2_stats :file`

`pileup_table :file`

`contamination_table :file`

`segmentation_table :file`

`filtered_vcf :file`

`filtered_tbi :file`

`filtered_stats :file`

included modules and subworkflows

maintainer

get in touch