nf-core/pacvar
Longread PacBio sequencing processing for WGS and PureTarget
Version history
nf-core/pacvar 1.1.0 - Neon tetra
nf-core/pacvar 1.1.0 expands the WGS workflow with major new PacBio long-read analysis capabilities, including copy number variant calling (hificnv), optional sawfish structural variant calling (sawfish), CpG methylation profiling (pb-CpG-tools), Fiber-seq processing (fibertools-rs), and VEP annotation for SNVs, indels, SVs, and CNVs (ensemblvep).
This release also adds optional fail BAM support (pbmerge) for the repeat workflow, including HiFi and fail BAM merging after mapping. The pipeline has been refreshed to nf-core/tools 4.0.2, with updated core nf-core modules, MultiQC integration, container configuration files, test profiles, documentation, and schema support.
Highlights include:
- New HiFiCNV copy number variant calling support with
hificnv - Optional
sawfishSV and CNV calling - CpG methylation profiling with
pb-CpG-tools - Fiber-seq support with
fibertools-rs - VEP annotation for SNVs, indels, SVs, and CNVs
- Optional VEP cache download support
- Optional fail BAM handling in the repeat workflow
- Updated nf-core template 4.0.2
- Updated tool versions, including DeepVariant, GATK4, pbsv, TRGT, MultiQC, samtools, bcftools, and others
This release substantially broadens pacvar’s PacBio variant discovery and annotation functionality while keeping the workflow aligned with current nf-core infrastructure.
Thanks to everyone who contributed to and reviewed this release.
Contributors: @chaochaowong, @stvdsomp, @tanyasarkjain
Reviewers: @vagkaratzas, @tanyasarkjain, @maxulysse, @nvnieuwk, @pinin4fjords, @YiJin-Xiong, @mashehu, @SPPearce
What’s Changed
- Changed files produced downstream from PBSV to have an output file name containing ‘sv’ to indicate origin of the files, as with those files downstream from GATK4 and Deepvariant have ‘snv’ in output file name
- Tweaks to the channels passed into HiPhase - specifically ensure that the inputted VCF and BAM channel are ordered in the same way (according to their shared meta).
nf-core/pacvar is a bioinformatics pipeline that processes long-read PacBio data. Specifically, the pipeline provides two workflows: one for processing whole-genome sequencing data, and another for processing reads from the PureTarget expansion panel offered by PacBio.
- Aligns raw BAM files, sorts and Indexes
- Variant calls (with GATK or Deepvariant)
- For repeat Regions - characterizes number of motifs and produces waterfall plots
Full Changelog: https://github.com/nf-core/pacvar/compare/v1.0.0…1.0.0