Description

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.

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
included modules and subworkflows
gatk4/mutect2 gatk4/getpileupsummaries gatk4/calculatecontamination gatk4/filtermutectcalls
maintainer
Github user GCJMackenzie
get in touch
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