Nextflow Modules
Showing module(s) with keyword "bcftools"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_variant_calling_mpileup_bcftools | Workflow | BAM genotype likelihoods bcftools | Subworkflow to compute genotype likelihoods from BAM files using bcftools/mpileup and bcftools/call variants by chromosomes. The resulting VCF files are then merged by chromosomes and annotated with bcftools/annotate to give an ID for each variants. During samples merging and region concatenation, all metadata will be preserved and stored in the key `metas` at each step. |
| nf-core/bcftools/annotate | Process | bcftools annotate vcf remove add | Add or remove annotations. |
| 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/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/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/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/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/query | Process | query variant calling bcftools VCF | Extracts fields from VCF or BCF files and outputs them in user-defined format. |
| 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/rhocall/viz | Process | roh bcftools runs_of_homozygosity | Call regions of homozygosity and make tentative UPD calls |
| nf-core/vcf_annotate_vepyr | Workflow | vcf annotation normalisation vep vepyr bcftools huggingface | Optionally download a vepyr cache from Hugging Face and normalise a VCF with bcftools norm, then annotate it with Ensembl VEP consequences using vepyr and return the bgzip VCF with its tabix index. Give the cache either as `ch_cache` or as a Hugging Face dataset in `val_hf_repo`, such as `biodatageeks/vepyr_116_GRCh38_ensembl`; setting both, or neither, is an error. The repository is downloaded once and shared across all samples. To pin the cache or download only some contigs, add `--revision` and `--include` to `HUGGINGFACE_DOWNLOAD`'s `ext.args`. A partial download must include every entity's manifest and all contigs present in the VCF: ``` withName: 'HUGGINGFACE_DOWNLOAD' { ext.args = "--revision <commit> --include '*/chr22.parquet' --include '*/chrom_manifest.json'" } ``` What bcftools norm does comes from `BCFTOOLS_NORM`'s `ext.args`. Keep its output bgzip VCF (`--output-type z`): `VEPYR_ANNOTATE` runs a single pipeline for B |