Nextflow Modules
Showing module(s) with keyword "VCF"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bcftools/call | Process | variant calling view bcftools VCF | This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option. |
| nf-core/bcftools/concat | Process | variant calling concat bcftools VCF | Concatenate VCF files |
| nf-core/bcftools/consensus | Process | variant calling consensus VCF | Compresses VCF files |
| nf-core/bcftools/filter | Process | variant calling filtering VCF | Filters VCF files |
| nf-core/bcftools/isec | Process | variant calling intersect union complement VCF BCF | Apply set operations to VCF files |
| nf-core/bcftools/merge | Process | variant calling merge VCF | Merge VCF files |
| nf-core/bcftools/mpileup | Process | variant calling mpileup VCF | Compresses VCF files |
| nf-core/bcftools/norm | Process | normalize norm variant calling VCF | Normalize VCF file |
| nf-core/bcftools/plotvcfstats | Process | visualization stats VCF | Plots the output of bcftools stats |
| nf-core/bcftools/plugintag2tag | Process | tag2tag bcftools VCF | Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD. |
| nf-core/bcftools/query | Process | query variant calling bcftools VCF | Extracts fields from VCF or BCF files and outputs them in user-defined format. |
| nf-core/bcftools/rohviz | Process | visualisation RoH VCF | Visualise the output of bcftools roh |
| nf-core/bcftools/sort | Process | sorting VCF variant calling | Sorts VCF files |
| nf-core/bcftools/stats | Process | variant calling stats VCF | Generates stats from VCF files |
| nf-core/bcftools/view | Process | variant calling view bcftools VCF | View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF |
| nf-core/rbt/vcfsplit | Process | genomics splitting VCF BCF variants | A tool for splitting VCF/BCF files into N equal chunks, including BND support |
| nf-core/vcf_impute_beagle5 | Workflow | VCF imputation beagle5 phasing | Subworkflow to impute VCF files using BEAGLE5 software. The subworkflow takes VCF files, phased reference panel, genetic maps and chunks region to perform imputation and outputs phased and imputed VCF files. Meta map of all channels, except ch_input, will be used to perform joint operations. "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/vcf_impute_minimac4 | Workflow | VCF imputation minimac4 phasing MSAV | Subworkflow to impute VCF files using MINIMAC4 software. The subworkflow takes VCF files, phased reference panel, and genetic maps to perform imputation and outputs phased and imputed VCF files. Meta map of all channels, except ch_input, will be used to perform joint operations. "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/vcf_phase_shapeit5 | Workflow | VCF phase shapeit5 haplotype | Subworkflow to phase a reference panel VCF file using SHAPEIT5. The panel is first chunked by chromosome by glimpse2/chunk (if no chunks provided), then genotypes are phased with shapeit5/phasecommon and finally the chunks are merged back together by shapeit5/ligate by chromosomes. Meta map of all channels will be used to perform joint operations. "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/vcftools | Process |