Nextflow Modules
Showing module(s) with keyword "mutect2"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_create_som_pon_gatk | Workflow | gatk4 mutect2 genomicsdbimport createsomaticpanelofnormals variant_calling genomicsdb_workspace panel_of_normals | 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. |
| 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/bam_tumor_only_somatic_variant_calling_gatk | Workflow | gatk4 mutect2 getpileupsummaries calculatecontamination filtermutectcalls variant_calling tumor_only filtered_vcf | 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. |
| nf-core/gatk4/filtermutectcalls | Process | filtermutectcalls filter gatk4 mutect2 vcf | Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve 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 |
| nf-core/gatk4/mergemutectstats | Process | gatk4 merge mutect2 mutectstats | Merges mutect2 stats generated on different intervals/regions |
| nf-core/gatk4/mutect2 | Process | gatk4 haplotype indels mutect2 snvs somatic | Call somatic SNVs and indels via local assembly of haplotypes. |
| nf-core/parabricks/mutectcaller | Process | variant vcf mutect2 mutect somatic | NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. |