Nextflow Modules
Showing module(s) with keyword "variants"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bedgovcf | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |
| nf-core/cadd | 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 | genome structural variants bcf | Call structural variants |
| nf-core/freyja/boot | 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 | variants fasta deconvolution wastewater | specify the relative abundance of each known haplotype |
| nf-core/freyja/update | database variants UShER | downloads new versions of the curated SARS-CoV-2 lineage file and barcodes |
| nf-core/freyja/variants | variants fasta wastewater | call variant and sequencing depth information of the variant |
| nf-core/gatk4/cnnscorevariants | cnnscorevariants gatk4 variants | Apply a Convolutional Neural Net to filter annotated variants |
| nf-core/ivar/variants | amplicon sequencing variants fasta | Call variants from a BAM file using iVar |
| nf-core/lofreq/alnqual | variant calling low frequency variant calling variants bam | Lofreq subcommand to for insert base and indel alignment qualities |
| nf-core/lofreq/callparallel | variant calling low frequency variant calling call variants | It predicts variants using multiple processors |
| nf-core/lofreq/indelqual | variant calling variants bam indel qualities | Inserts indel qualities in a BAM file |
| nf-core/lofreq/somatic | 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 | 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/plink2/filter | plink2 filter samples variants missingness qualty | Filters plink bfiles or pfiles with filters such as maf or var |
| nf-core/plink/epistasis | interactions variants regression | Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. |
| nf-core/plink/fastepistasis | interactions variants regression | Fast Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. |
| nf-core/plink/ld | genetics associations variants | LD analysis in PLINK examines genetic variant associations within populations |
| nf-core/pypgx/createinputvcf | pypgx Pharmacogenetics variants | Call SNVs/indels from BAM files for all target genes. |
| nf-core/rbt/vcfsplit | genomics splitting VCF BCF variants | A tool for splitting VCF/BCF files into N equal chunks, including BND support |