ExternalExomeReprocessing_develop

3.3.1

2024-09-17 (Date of Last Commit)

• Updated DRAGEN aligner parameters to fix non-determinism; this does not affect the Exome workflow

ExomeReprocessing_develop

3.3.1

2024-09-17 (Date of Last Commit)

• Updated DRAGEN aligner parameters to fix non-determinism; this does not affect the exome workflow

ExomeGermlineSingleSample_develop

3.2.1

2024-09-17 (Date of Last Commit)

• Updated DRAGEN aligner parameters to fix non-determinism; this does not affect the Exome workflow

UltimaGenomicsJointGenotyping_develop

1.2.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling; this has no effect on this pipeline

JointGenotyping_develop

1.7.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling
• If target interval list is provided for filtering, the documentation in the header will be clearer
• If VETS is enabled, the SCORE annotation will be added to all output variants (even hard filtered sites)

JointGenotypingByChromosomePartTwo_develop

1.5.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling; this has no effect on this pipeline

JointGenotypingByChromosomePartOne_develop

1.5.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling; this has no effect on this pipeline

SmartSeq2SingleSample_develop

5.1.21

2024-09-11 (Date of Last Commit)

• Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the SmartSeq2SingleSample pipeline

MultiSampleSmartSeq2_develop

2.2.22

2024-09-11 (Date of Last Commit)

• Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the MultiSmartSeq2 pipeline

WholeGenomeReprocessing_v3.3.0

3.3.0

2024-09-06 (Date of Last Commit)

• Updated to GATK version 4.6.0.0
• Updated version drops some low quality sites from VCFs; if reblocking is enabled, the DP annotation in some ref blocks will change due to the change in HaplotypeCaller