Nextflow Modules
Showing module(s) with keyword "BAM"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_dedup_umi | Workflow | deduplication UMI BAM genome transcriptome umicollapse umitools | BAM deduplication with UMI processing for both genome and transcriptome alignments |
| nf-core/bam_impute_quilt | Workflow | BAM imputation quilt | Subworkflow to impute BAM files using QUILT software. Variants location to impute are obtain through the tsv file given. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |
| nf-core/bam_impute_stitch | Workflow | BAM imputation stitch | Subworkflow to impute BAM files using STITCH software. Variants location to impute are obtain through the legend file given. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |
| nf-core/bamreadcount | Process | BAM CRAM metrics genomics | bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. |
| nf-core/bam_variant_calling_mpileup_bcftools | Workflow | BAM genotype likelihoods bcftools | Subworkflow to compute genotype likelihoods from BAM files using bcftools/mpileup and bcftools/call variants by chromosomes. The resulting VCF files are then merged by chromosomes and annotated with bcftools/annotate to give an ID for each variants. During samples merging and region concatenation, all metadata will be preserved and stored in the key `metas` at each step. |
| nf-core/biscuit/qc | Process | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index BAM quality control | Perform basic quality control on a BAM file generated with Biscuit |
| 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/fastdup | Process | duplicate BAM reads | FastDup is a tool designed to locate and tag duplicate reads in a coordinate-sorted SAM or BAM file, using the same core algorithm as Picard MarkDuplicates. |
| nf-core/smncopynumbercaller | Process | 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. |