Nextflow Modules
Showing module(s) with keyword "copy number"
| Module | Keywords | Description |
|---|---|---|
| nf-core/ascat | bam copy number cram | copy number profiles of tumour cells. |
| nf-core/cnaqc | WGS copy number quality control | Quality control of copy number data from bulk WGS assays |
| nf-core/cnvkit/access | cvnkit access fasta copy number | Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file. |
| nf-core/cnvkit/antitarget | cvnkit antitarget cnv copy number | Derive off-target (“antitarget”) bins from target regions. |
| nf-core/cnvkit/batch | cnvkit bam fasta copy number | Copy number variant detection from high-throughput sequencing data |
| nf-core/cnvkit/call | cnvkit bam fasta copy number | Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number |
| nf-core/cnvkit/export | cnvkit copy number export | Convert copy number ratio tables (.cnr files) or segments (.cns) to another format. |
| nf-core/cnvkit/genemetrics | cnvkit bam fasta copy number | Copy number variant detection from high-throughput sequencing data |
| nf-core/cnvkit/reference | cnvkit reference cnv copy number | Compile a coverage reference from the given files (normal samples). |
| nf-core/cnvkit/target | cnvkit target cnv copy number | Transform bait intervals into targets more suitable for CNVkit. |
| nf-core/gatk4/determinegermlinecontigploidy | copy number counts determinegermlinecontigploidy gatk4 | Determines the baseline contig ploidy for germline samples given counts data |
| nf-core/gatk4/postprocessgermlinecnvcalls | copy number gatk4 postprocessgermlinecnvcalls | Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios |
| nf-core/sequenzautils/bam2seqz | sequenzautils copy number bam2seqz | Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file |
| nf-core/sequenzautils/gcwiggle | sequenzautils copy number gc_wiggle | Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size. |
| nf-core/smncopynumbercaller | copy number BAM CRAM SMN1 SMN2 | tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file. |