v2.0.0-rc5

• Bugfix: GLnexus was previously joint-calling from VCF input rather than gVCF. This has been fixed.
• The family.wdl entrypoint can now be used for both single sample (singleton) and multisample (duo, trio, quad, etc.) inputs, allowing for a single workflow to be used for all analyses. The per-sample outputs will be arrays in the same order as the sample input. The singleton.wdl entrypoint will continue to be maintained for backends that need flattened inputs and outputs.
• Added cumulative distribution plot for aligned read depth.
• Added mapped_read_count as a stat output.
• Renamed some output keys and filenames for clarity or better sorting.

Version updates:

• pb-StarPhase v0.14.2, database 20240826
• HiPhase v1.4.5
• TRGT v1.2.0
• mosdepth v0.3.9
• slivar v0.3.1

Full Changelog: v2.0.0-rc4...v2.0.0-rc5

v2.0.0-rc4

Updated pbstarphase to v0.14.1 and correctly set pbstarphase task disk size requirements.
Refactored code for parallelizing pbsv call. (Related to HealthOmics support.)
Modified bcftools.split_vcf_by_sample to support Terra.
Modified write_ped_phrank task for uniform interface with both singleton and family workflows.
Updated documentation.
Updated HiPhase to v1.4.4

For more detailed notes on v2, check the release notes for v2.0.0-rc2.

Full Changelog: v2.0.0-rc2...v2.0.0-rc4

v1.2.0

What's Changed

• Updated to HiPhase v1.4.4. by @williamrowell in #148

Full Changelog: v1.1.1...v1.2.0

v2.0.0-rc2

This is a pre-release workflow. Please do not depend on this for production analysis.

This release is not supported by the PacBio Tech Support or Field Support teams. Please only use this if you are already in contact with PacBio R&D and providing active feedback on performance and results.

This is a major rewrite of the v1 workflow. Please read the documentation before filing issues.

Structural changes:

• There are two entry-points, singleton.wdl and family.wdl.
  • singleton has a flattened input/output structure that should have better compatibility with platforms like Terra.
  • family includes joint calling tasks for small variants and structural variants.
  • phenotype field has been changed from Array[String] to String, a comma-delimited string, e.g., "HP:0000118,HP:0000001"
• Static inputs like reference FASTA and BED files are now referenced through new "map" files to simplify inputs.json structure.
• Most tasks have been moved to the wdl-common submodule for reuse.
• AWS AGC has been deprecated by AWS, and support has been removed.
• AWS HealthOmics support has been added (needs improved documentation).

New features:

• If aligned BAMs are provided as input to the workflow, alignment and phasing information should be stripped. If the input BAM has consensus kinetics tags, these will be stripped as well. This needs better testing. *introduced in rc2
• HiPhase now jointly phases small variants (DeepVariant), structural variants (PBSV), and tandem repeats (TRGT).
• A merged TRGT VCF will be generated by the family workflow. *updated in rc2
• Pharmacogenomics analysis with StarPhase and PharmCAT.
• Updated tertiary analysis with gnomAD v4.1 and CoLoRSdb population datasets.
• High level summary statistics (e.g., mean depth, variant counts by type, etc) output directly by workflow.
• Plots for read length and quality histograms.
• Inferred sex by relative chrY aligned depth. This will never override user-defined sex, but is used if the sex is not provided by user.
• Memory has been increased for DeepVariant postprocess_variants. *updated in rc2

Tool updates

DeepVariant v1.6.1
Paraphase v3.1.1
TRGT v1.1.1 *updated in rc2
HiPhase v1.4.3 *updated in rc2
HiFiCNV v1.0.0
pb-StarPhase v0.13.2 *updated in rc2
PharmCAT v2.15.0 *updated in rc2
CoLoRSdb v1.1.0 *updated in rc2

v2.0.0-rc1

This is a pre-release workflow. Please do not depend on this for production analysis.

This release is not supported by the PacBio Tech Support or Field Support teams. Please only use this if you are already in contact with PacBio R&D and providing active feedback on performance and results.

This is a major rewrite of the v1 workflow. Please read the documentation before filing issues.

Structural changes:

• There are two entrypoints, singleton.wdl and family.wdl.
  • singleton has a flattened input/output structure that should have better compatibility with platforms like Terra.
  • family includes joint calling tasks for small variants and structural variants.
  • phenotype field has been changed from Array[String] to String, a comma-delimited string, e.g., "HP:0000118,HP:0000001"
• Static inputs like reference FASTA and BED files are now referenced through new "map" files to simplify inputs.json structure.
• Most tasks have been moved to the wdl-common submodule for reuse.
• AWS AGC has been deprecated by AWS, and support has been removed.
• AWS HealthOmics support has been added (needs improved documentation).

New features:

• HiPhase now jointly phases small variants (DeepVariant), structural variants (PBSV), and tandem repeats (TRGT).
• Pharmacogenomics analysis with StarPhase and PharmCat.
• Updated tertiary analysis with gnomAD v4.1 and CoLoRSdb population datasets.
• High level summary statistics (e.g., mean depth, variant counts by type, etc) output directly by workflow.
• Plots for read length and quality histograms.
• Inferred sex by relative chrY aligned depth. This will never override user-defined sex, but is used if the sex is not provided by user.

Tool updates:

• Paraphase v3.1.1
• TRGT v1.0.0
• HiPhase v1.4.2
• HiFiCNV v1.0.0

Full Changelog: v1.1.1...v2.0.0-rc1

Contributors:
@juniper-lake
@gconcepcion
@amwenger

v1.1.1

What's Changed

• docs: Changed image references from relative to absolute so that they can be rendered correctly in DockStore. in #110
• Fix: Previously, pedigree creation passed the cohort information through a transient yaml step where parents were set implicitly based on order. There was a typo in this that swapped mom and dad, and assumed that single parental info always came from mom. Pedigree is now created directly from cohort json structure and mom and dad are set explicitly. Closes #129 (@juniper-lake)
• Previously, the svpack tagzygosity function annotated variants with hom/het genotypes for any samples. Now, it only annotates variants with zygosity for affected samples. The svpack filtered/annotated TSV will only include variants that are included in at least one affected sample. PacificBiosciences/svpack#13 (@amwenger)
• Fixed typo in HPC backend README. Closes #121

Full Changelog: v1.1.0...v1.1.1

v1.1.0

What's Changed

• Updated documentation with a logo and a note about the requirement for a container rumtime.
• Updated to HiPhase v1.0.0, which addresses some edge case bugs.

Full Changelog: v1.0.3...v1.1.0

v1.0.3

What's Changed

• Fix for concat_vcf for miniwdl. Link all inputs into a single directory so that vcfs and indices are together. by @williamrowell in #77

Full Changelog: v1.0.2...v1.0.3

v1.0.2

What's Changed

• Replaced WhatsHap with HiPhase for concurrent small variant and large indel phasing and alignment haplotagging.
• Split pbsv call into ~14 equally sized chunks for improved wall time, especially during joint calling.
• Several tools have been updated to newer versions, including TRGT, HiFiCNV, and pb-cpg-tools.
• Additionally output raw bcftools roh output in addition to the simplified bed file.
• Fixed path errors in inputs templates.
• Tertiary analysis is disabled by default, and tertiary analysis inputs are optional.

v0.9.0-beta

Merge pull request #48 from PacificBiosciences/develop