Nextflow Modules
Showing module(s) with keyword "vcf"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/aardvark/compare | Process | variant calling benchmarking vcf comparison consensus | A tool to evaluate variant calling performance by comparing a query VCF against a truth VCF. |
| nf-core/aardvark/merge | Process | variant calling vcf comparison consensus merging | A tool to evaluate and merge multiple variant calls into a consensus VCF. |
| nf-core/annotsv/annotsv | Process | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/atlas/call | Process | atlas variant calling vcf population genetics | generate VCF file from a BAM file using various calling methods |
| nf-core/bam_impute_quilt2 | Workflow | bam cram imputation quilt quilt2 vcf | Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |
| 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/bcftools/annotate | Process | bcftools annotate vcf remove add | Add or remove annotations. |
| nf-core/bcftools/convert | Process | bcftools convert vcf gvcf | Converts certain output formats to VCF |
| nf-core/bcftools/csq | Process | annotation gff gff3 protein functional vcf bcf bcftools | bcftools Haplotype-aware consequence caller |
| nf-core/bcftools/index | Process | vcf index bcftools csi tbi | Index VCF tools |
| nf-core/bcftools/pluginfilltags | Process | info bcftools tags vcf | Compute and fill various INFO tags |
| nf-core/bcftools/pluginfixploidy | Process | 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 | Process | 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 | Process | scatter vcf bcf genomics | Split VCF by chunks or regions, creating multiple VCFs. |
| nf-core/bcftools/pluginsetgt | Process | 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 | Process | split vcf genomics | Split VCF by sample, creating single- or multi-sample VCFs. |
| nf-core/bcftools/pluginvcf2table | Process | bcftools vcf table variant calling | Converts VCF/BCF files into a tab-delimited table using the bcftools +vcf2table plugin. Each variant is output as one row, with INFO and FORMAT fields as columns. |
| nf-core/bcftools/reheader | Process | reheader vcf update header | Reheader a VCF file |
| nf-core/bcftools/split | Process | vcf split genomics | Split a vcf file into files per chromosome |
| nf-core/bedgovcf | Process | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |