Nextflow Modules
Showing module(s) with keyword "cnv"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_cnv_wisecondorx | Workflow | cnv bam bed cram plots genomics | A subworkflow for calling CNVs using WisecondorX |
| nf-core/cnvkit/antitarget | Process | cvnkit antitarget cnv copy number | Derive off-target (“antitarget”) bins from target regions. |
| nf-core/cnvkit/reference | Process | cnvkit reference cnv copy number | Compile a coverage reference from the given files (normal samples). |
| nf-core/cnvkit/target | Process | cnvkit target cnv copy number | Transform bait intervals into targets more suitable for CNVkit. |
| nf-core/cnvnator/cnvnator | Process | cnvnator cnv cna | CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads. |
| nf-core/cnvnator/convert2vcf | Process | cnvnator cnv cna | convert2vcf.pl is command line tool to convert CNVnator calls to vcf format. |
| nf-core/cnvpytor/importreaddepth | Process | read depth cnv cna call | command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file. |
| nf-core/cnvpytor/partition | Process | cnv call partition histogram | Calculate segmentation for specified bin size (multiple bin sizes separate by space) |
| nf-core/cnvpytor/view | Process | cnv calling vcf | view function to generate vcfs |
| nf-core/controlfreec/assesssignificance | Process | cna cnv somatic single tumor-only | Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC |
| nf-core/controlfreec/freec | Process | cna cnv somatic single tumor-only | Copy number and genotype annotation from whole genome and whole exome sequencing data |
| nf-core/controlfreec/freec2bed | Process | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/freec2circos | Process | cna cnv somatic single tumor-only | Format Freec output to circos input format |
| nf-core/controlfreec/makegraph | Process | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/makegraph2 | Process | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/goleft/indexcov | Process | coverage cnv genomics depth | Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome. |
| nf-core/hificnv | Process | copy number variation cnv PacBio HiFi long reads structural variation | Copy number variant calling from PacBio HiFi reads |
| nf-core/hmmcopy/gccounter | Process | hmmcopy gccounter cnv | gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference |
| nf-core/hmmcopy/mapcounter | Process | hmmcopy mapcounter cnv | mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file |