Nextflow Modules
Showing module(s) with keyword "variant"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_variant_calling_sort_freebayes_bcftools | Workflow | variant sort index bam cram vcf | Call variants using freebayes, then sort and index |
| nf-core/clair3 | Process | germline variant Indel SNV | Clair3 is a germline small variant caller for long-reads |
| nf-core/ferrohgvs/normalize | Process | hgvs variant normalize nomenclature canonical | Normalize HGVS variant descriptions to canonical form with ferro |
| nf-core/ferrohgvs/parse | Process | hgvs variant parse validation nomenclature | Parse and validate HGVS variant descriptions with ferro |
| nf-core/graphtyper/genotype | Process | variant vcf bam cram pangenome | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/graphtyper/vcfconcatenate | Process | combine concatenate variant vcf | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/igvreports | Process | vcf variant genomics | A Python application to generate self-contained HTML reports for variant review and other genomic applications |
| nf-core/jvarkit/vcffilterjdk | Process | vcf bcf filter variant java script | Filtering VCF with dynamically-compiled java expressions |
| nf-core/nextclade/datasetget | Process | nextclade variant consensus | Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/nextclade/run | Process | nextclade variant consensus | SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/octopusv/correct | Process | structural variant sv svcf normalize | Standardize a caller VCF into OctopuSV SVCF format. |
| nf-core/octopusv/filter | Process | structural variant sv svcf filter | Filter SVCF based on specified criteria |
| nf-core/octopusv/subset | Process | structural variant sv svcf subset | Subset an OctopuSV SVCF by sample and/or caller. |
| nf-core/parabricks/deepsomatic | Process | variant somatic vcf deepsomatic tumor normal | NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating deepsomatic. |
| nf-core/parabricks/deepvariant | Process | variant deep variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant. |
| nf-core/parabricks/haplotypecaller | Process | variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller. |
| nf-core/parabricks/mutectcaller | Process | variant vcf mutect2 mutect somatic | NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. |
| nf-core/pbsv/call | Process | variant pacbio genomics | pbsv/call - PacBio structural variant (SV) calling and analysis tools |
| nf-core/pbsv/discover | Process |