Nextflow Modules
Showing module(s) with keyword "vcf"
| Module | Keywords | Description |
|---|---|---|
| nf-core/annotsv/annotsv | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/atlas/call | atlas variant calling vcf population genetics | generate VCF file from a BAM file using various calling methods |
| nf-core/bcftools/annotate | bcftools annotate vcf remove add | Add or remove annotations. |
| nf-core/bcftools/convert | bcftools convert vcf gvcf | Converts certain output formats to VCF |
| nf-core/bcftools/csq | annotation gff gff3 protein functional vcf bcf bcftools | bcftools Haplotype-aware consequence caller |
| nf-core/bcftools/index | vcf index bcftools csi tbi | Index VCF tools |
| nf-core/bcftools/pluginfilltags | info bcftools tags vcf | Compute and fill various INFO tags |
| nf-core/bcftools/pluginfixploidy | fixploidy bcftools ploidy vcf | The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes. |
| nf-core/bcftools/pluginimputeinfo | impute-info bcftools imputation metrics tags vcf | Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. |
| nf-core/bcftools/pluginscatter | scatter vcf bcf genomics | Split VCF by chunks or regions, creating multiple VCFs. |
| nf-core/bcftools/pluginsetgt | setgt bcftools genotype vcf | Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that. |
| nf-core/bcftools/pluginsplit | split vcf genomics | Split VCF by sample, creating single- or multi-sample VCFs. |
| nf-core/bcftools/reheader | reheader vcf update header | Reheader a VCF file |
| nf-core/bcftools/split | vcf split genomics | Split a vcf file into files per chromosome |
| nf-core/bedgovcf | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |
| nf-core/bedtools/closest | bedtools closest bed vcf gff | For each feature in A, finds the closest feature (upstream or downstream) in B. |
| nf-core/bedtools/complement | bed gff vcf complement bedtools intervals | Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. |
| nf-core/bedtools/coverage | bedtools coverage bam bed gff vcf histogram | computes both the depth and breadth of coverage of features in file B on the features in file A |
| nf-core/bedtools/jaccard | vcf gff bed jaccard intersection union statistics | Calculate Jaccard statistic b/w two feature files. |
| nf-core/bedtools/map | bed vcf< |