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.
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
One BAM or CRAM file with its index, plus an empty placeholder for the
optional matched normal sample, which is not used in tumour only mode.
Structure: [ val(meta), path(input), path(input_index), [] ]
*.{bam,cram}Index of the reference fasta file, plus the index of the bgzipped fasta
if it is compressed.
Structure: [ val(meta2), path(fai), path(gzi) ]
*.fasta.faivcf file to be used to force-call alleles.
Structure: [ val(meta3), path(alleles) ]
*.vcf.gzIndex file for alleles to be force-called.
Structure: [ val(meta4), path(alleles_tbi) ]
*.vcf.gz.tbiPopulation vcf of germline sequencing, containing allele fractions.
Structure: [ val(meta5), path(germline_resource) ]
*.vcf.gzIndex file for the germline resource.
Structure: [ val(meta6), path(germline_resource_tbi) ]
*.vcf.gz.tbivcf file to be used as a panel of normals.
Structure: [ val(meta7), path(panel_of_normals) ]
*.vcf.gzIndex for the panel of normals.
Structure: [ val(meta8), path(panel_of_normals_tbi) ]
*.vcf.gz.tbiOutput
File containing the contamination table.
Structure: [ val(meta), path(contamination_table) ]
*.contamination.tableFile containing statistics of the filtermutectcalls run.
Structure: [ val(meta), path(filtered_stats) ]
*.filteringStats.tsvtbi file that pairs with the filtered vcf.
Structure: [ val(meta), path(filtered_tbi) ]
*.vcf.gz.tbiFile containing filtered mutect2 calls.
Structure: [ val(meta), path(filtered_vcf) ]
*.vcf.gzStats file for the mutect2 vcf.
Structure: [ val(meta), path(mutect2_stats) ]
*.vcf.gz.statsCompressed vcf file to be used for variant_calling.
Structure: [ val(meta), path(mutect2_vcf) ]
*.vcf.gzFile containing the pileup summary table.
Structure: [ val(meta), path(pileup_table) ]
*.pileups.tableincluded modules and subworkflows
maintainer
