Nextflow Modules
Showing module(s) with keyword "bcftools"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bcftools/annotate | bcftools annotate vcf remove add | Add or remove annotations. |
| nf-core/bcftools/call | 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 | variant calling concat bcftools VCF | Concatenate VCF files |
| 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/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/plugintag2tag | 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 | query variant calling bcftools VCF | Extracts fields from VCF or BCF files and outputs them in user-defined format. |
| nf-core/bcftools/view | 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/rhocall/viz | roh bcftools runs_of_homozygosity | Call regions of homozygosity and make tentative UPD calls |