Description

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.

Input

Name (Type)
Description
Pattern

ch_mutect2_in (list)

An input channel containing the following files:

  • input: One or more BAM/CRAM files
  • input_index: The index/indices from the BAM/CRAM file(s)
  • interval_file: An interval file to be used with the mutect call
    Structure: [ meta, input, input_index, interval_file ]

fasta (file)

The reference fasta file

*.fasta

fai (file)

Index of reference fasta file

*.fasta.fai

dict (file)

GATK sequence dictionary

*.dict

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

mutect2_vcf (list)

List of compressed vcf files to be used to make the gendb workspace

[ *.vcf.gz ]

mutect2_index (list)

List of indexes of mutect2_vcf files

[ *vcf.gz.tbi ]

mutect2_stats (list)

List of stats files that pair with mutect2_vcf files

[ *vcf.gz.stats ]

genomicsdb (directory)

Directory containing the files that compose the genomicsdb workspace.

path/name_of_workspace

pon_vcf (file)

Panel of normal as compressed vcf file

*.vcf.gz

pon_index (file)

Index of pon_vcf file

*vcf.gz.tbi
included in
createpanelrefs
included modules and subworkflows
gatk4/mutect2 gatk4/genomicsdbimport gatk4/createsomaticpanelofnormals
maintainer
Github user GCJMackenzie
get in touch
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