Nextflow Modules
Showing module(s) with keyword "variants"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_variant_demix_boot_freyja | Workflow | bam variants cram | Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference) |
| nf-core/bedgovcf | Process | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |
| nf-core/cadd | Process | cadd annotate variants | CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. |
| nf-core/delly/call | Process | genome structural variants bcf | Call structural variants |
| nf-core/delly/sr | Process | genome structural variants bcf | Integrated structural variant (SV) prediction method |
| nf-core/freyja/boot | Process | variants fasta deconvolution wastewater bootstrapping | Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth. |
| nf-core/freyja/demix | Process | variants fasta deconvolution wastewater | specify the relative abundance of each known haplotype |
| nf-core/freyja/update | Process | database variants UShER | downloads new versions of the curated SARS-CoV-2 lineage file and barcodes |
| nf-core/freyja/variants | Process | variants fasta wastewater | call variant and sequencing depth information of the variant |
| nf-core/gatk4/cnnscorevariants | Process | cnnscorevariants gatk4 variants | Apply a Convolutional Neural Net to filter annotated variants |
| nf-core/holodeck/mutate | Process | simulation vcf mutations variants benchmarking | Generate a VCF of random mutations from a reference genome with holodeck |
| nf-core/ivar/variants | Process | amplicon sequencing variants fasta | Call variants from a BAM file using iVar |
| nf-core/kled | Process | genomics longread structural variants | An ultra-fast and sensitive structural variant detection tool for long-read sequencing data. |
| nf-core/lofreq/alnqual | Process | variant calling low frequency variant calling variants bam | Lofreq subcommand to for insert base and indel alignment qualities |
| nf-core/lofreq/callparallel | Process | variant calling low frequency variant calling call variants | It predicts variants using multiple processors |
| nf-core/lofreq/indelqual | Process | variant calling variants bam indel qualities | Inserts indel qualities in a BAM file |
| nf-core/lofreq/somatic | Process | variant calling low frequency variant calling somatic variants vcf | Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available |
| nf-core/lofreq/viterbi | Process | variant calling low frequency variant calling variants bam probabilistic realignment | Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available |
| nf-core/mgatk/call | Process | mitochondria mtDNA variants ATAC-seq | Call mitochondrial variants and generate mitochondrial |