Nextflow Modules
Showing module(s) with keyword "variant calling"
| 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/atlas/call | Process | atlas variant calling vcf population genetics | generate VCF file from a BAM file using various calling methods |
| 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/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/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/biscuit/pileup | Process | bisulfite DNA methylation pileup variant calling WGBS scWGBS bam vcf | Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants |
| nf-core/deepsomatic | Process | variant calling machine learning neural network | DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file. |
| nf-core/deepvariant/callvariants | Process | variant calling machine learning neural network | Call variants from the examples produced by make_examples |
| nf-core/deepvariant/makeexamples | Process | variant calling machine learning neural network | Transforms the input alignments to a format suitable for the deep neural network variant caller |