Nextflow Modules
Showing module(s) with keyword "learnreadorientationmodel"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_tumor_normal_somatic_variant_calling_gatk | Workflow | gatk4 mutect2 learnreadorientationmodel getpileupsummaries calculatecontamination filtermutectcalls variant_calling tumor_only filtered_vcf | 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. |
| nf-core/gatk4/learnreadorientationmodel | Process | gatk4 learnreadorientationmodel mutect2 readorientationartifacts | Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts |