Description
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.
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) ]
Population vcf of germline sequencing, containing allele fractions.
Structure: [ path(germline_resources) ]
Index file for the germline resource.
Structure: [ path(germline_resources_tbi) ]
Vcf file to be used as a panel of normals.
Structure: [ path(panel_of_normals) ]
Output
File containing information to be passed to LearnReadOrientationModel.
Structure: [ val(meta), path(f1r2) ]
File containing artifact-priors to be used by filtermutectcalls.
Structure: [ val(meta), path(artifact_priors) ]
File containing the tumor pileup summary table, kept separate as calculatecontamination needs them individually specified.
Structure: [ val(meta), path(table) ]
File containing the normal pileup summary table, kept separate as calculatecontamination needs them individually specified.
Structure: [ val(meta), path(table) ]
Output table containing segmentation of tumor minor allele fractions.
Structure: [ val(meta), path(table) ]
