v0.14-beta

Updated pre-release of cohort pipeline for Terra. Changes include:

• Switch to single cohort-level ped file rather than batch ped files
• Add functionality to randomly subsample input samples in trainGCNV
• Bug fixes to FORMAT EV field
• Updates to Module07-Module10

v0.13.1-beta Minor updates to v0.13-beta

• Fixes to Module07
• Minor changes to re-genotype filtering in Module04b for smaller cohorts

v0.13-beta

Updated pre-release of batch pipeline for Terra, incorporating changes such as:

• Make outlier cutoff table input to Module03 optional to better reflect use case
• Bug fixes and performance improvements to Module04b
• Break-up of Module0506 into sub-workflows
• Fix handling of MEI SVTYPE in Module07
• Changes reflected in v0.12-beta release

v0.12-beta

This release upgrades the single sample pipeline to work with the upgrades to gCNV and median-based re-genotyping that were implemented in the joint pipeline. Other changes include:

• Generates input JSON files and the single-sample pipeline Terra workspace files from templates
• Allows optional inputs of precomputed module00a files for the single sample pipeline
• Bug fixes for module 03 and MasterVcfQC
• Improved resource acquisition and monitoring scripts
• Implements a sample wide QC step in the single sample pipeline for samples that are outliers in coverage or WGD score

Pre-release of batch pipeline

Pre-release of batch pipeline for upcoming GATK-SV Terra workspace

v0.9.1-beta-hotfix

Hotfix includes only the new bug fix for empty shards in Module07

v0.10-beta

Additional fixes to single sample pipeline edge cases.

Upgrades gCNV to v4.1.8.1

v0.9.1-beta Fixes for edge cases in single sample pipeline

This release includes several bug fixes for v0.9-beta, most of which handle data conditions which result in empty shards that could cause workflow failures.

Single Sample Pipeline improvements

This pre-release of the single sample pipeline contains several improvements:

• PESR collection has been changed from svtk collect-pesr to GATK PairedEndAndSplitReadEvidenceCollection. This should fix a rare issue observed on some samples in which PESR records appear out of order and are not consolidated into single rows. (#34)
• Moves WDL parameters to the new nomenclature of include and exclude lists (#29)
• Fixes invalid VCF headers (#41)
• In the final single sample VCF output, reports reciprocal translocation events using a set of BND records linked by EVENT_ID (#36)
• Adds annotation with gnomAD allele frequencies to the Single Sample pipeline, and provides an additional output in BED format.

Hotfix 2 for v0.8

This fixes an issue in WHAM processing and standardization that stemmed from incomplete substituting of sample IDs that was causing all variants from WHAM to be lost.