Nextflow Modules
Showing module(s) with keyword "variant_calling"
| 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_normal_somatic_variant_calling_strelka | Workflow | strelka variant_calling filtered_vcf | Perform variant calling on a paired tumor normal set of samples using strelka somatic 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/sentieon/dnascope | Process | dnascope sentieon variant_calling | DNAscope algorithm performs an improved version of Haplotype variant calling. |
| nf-core/sentieon/tnhaplotyper2 | Process | tnseq tnhaplotyper2 sentieon variant_calling | Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs. |
| nf-core/sentieon/tnscope | Process | tnscope sentieon variant_calling | TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm. |