Nextflow Modules
Showing module(s) with keyword "variant"
| Module | Keywords | Description |
|---|---|---|
| nf-core/clair3 | germline variant Indel SNV | Clair3 is a germline small variant caller for long-reads |
| nf-core/graphtyper/genotype | variant vcf bam cram pangenome | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/graphtyper/vcfconcatenate | combine concatenate variant vcf | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/igvreports | vcf variant genomics | A Python application to generate self-contained HTML reports for variant review and other genomic applications |
| nf-core/jvarkit/vcffilterjdk | vcf bcf filter variant java script | Filtering VCF with dynamically-compiled java expressions |
| nf-core/nextclade/datasetget | nextclade variant consensus | Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/nextclade/run | nextclade variant consensus | SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/parabricks/deepvariant | variant deep variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant. |
| nf-core/parabricks/haplotypecaller | variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller. |
| nf-core/parabricks/mutectcaller | variant vcf mutect2 mutect somatic | NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. |
| nf-core/pbsv/call | variant pacbio genomics | pbsv/call - PacBio structural variant (SV) calling and analysis tools |
| nf-core/pbsv/discover | variant pacbio structural | pbsv - PacBio structural variant (SV) signature discovery tool |
| nf-core/platypus | variant call dna genetic | Platypus is a tool that efficiently and accurately calling genetic variants from next-generation DNA sequencing data |
| nf-core/plink/vcf | plink vcf variant call | Analyses variant calling files using plink |
| nf-core/snippy/run | variant fastq bacteria | Rapid haploid variant calling |
| nf-core/snpeff/download | annotation effect prediction snpeff variant vcf | Genetic variant annotation and functional effect prediction toolbox |
| nf-core/snpeff/snpeff | annotation effect prediction snpeff variant vcf | Genetic variant annotation and functional effect prediction toolbox |
| nf-core/snpsift/annmem | vcf annotation snpsift variant database | Annotate VCF files using pre-built SnpSift annMem databases. Enriches input VCF records by querying memory-optimized indexed dataframes for high-performance annotation. |
| nf-core/snpsift/annmemcreate | vcf annotation snpsift variant database | Create memory-optimized SnpSift vardb databases from VCF files for use with SnpSift annMem annotation. Converts VCF files (e.g. ClinVar, dbSNP, Cosmic) into indexed dataframes for fast lookup. |
| nf-core/variantextractor | vcf variant structural variant normalization homogenization | Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files. Homogenizes multiallelic variants, MNPs and SVs (including imprecise paired breakends and single breakends) to facilitate downstream processing. |