nf-core/pacvar
Longread PacBio sequencing processing for WGS and PureTarget
alignmentlong-readpacbiopuretargetvariant-callingwgs
Version history
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