Nextflow Modules
Showing module(s) with keyword "cnvkit"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/cnvkit/batch | Process | cnvkit bam fasta copy number | Copy number variant detection from high-throughput sequencing data |
| nf-core/cnvkit/call | Process | cnvkit bam fasta copy number | Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number |
| nf-core/cnvkit/coverage | Process | cnvkit coverage BAM CRAM bedGraph read depth genomics | Calculate coverage in the given regions from BAM/CRAM or bedGraph files read depths. |
| nf-core/cnvkit/export | Process | cnvkit copy number export | Convert copy number ratio tables (.cnr files) or segments (.cns) to another format. |
| nf-core/cnvkit/fix | Process | cnvkit fix cnn GC content bias RepeatMasker genomics | Combine the uncorrected target and antitarget coverage tables (.cnn) and correct for biases in regional coverage and GC content, according to the given reference. |
| nf-core/cnvkit/genemetrics | Process | cnvkit bam fasta copy number | Copy number variant detection from high-throughput sequencing data |
| nf-core/cnvkit/purity | Process | cnvkit purity ploidy cns genomics | estimates tumor purity and ploidy from a .cnr/.cns pair, using the same grid-search likelihood model as the somatic HMM methods. |
| nf-core/cnvkit/reference | Process | cnvkit reference cnv copy number | Compile a coverage reference from the given files (normal samples). |
| nf-core/cnvkit/segment | Process | cnvkit segment cbs haar hmm hmm-tumor hmm-germline none cnr genomics | Infer discrete copy number segments from the given coverage table. |
| nf-core/cnvkit/target | Process | cnvkit target cnv copy number | Transform bait intervals into targets more suitable for CNVkit. |