broadinstitute/gatk-sv: v0.27.3-beta
Year: 2023
Type: software
Abstract: GATK-SV v1.1 includes major single-sample pipeline upgrades such as improved filtering and a new reference panel, alongside updates to the joint calling pipeline. Updates include Single-sample pipeline Single-sample pipeline updates Add filtering New reference panel Run Scramble by default Reference panel creation notebook and more Revert format detection changes to MakeBincovMatrix Joint-calling pipeline functionality Enable DRAGEN-SV as a caller in cohort mode Enable outlier sample exclusion from training in TrainGCNV and GenerateBatchMetrics Add denoised copy number plots and stratified variant counts to EvidenceQc outputs Minor changes and bug fixes Zip regeno coverage medians file Update SVConcordance.wdl to enable stratified matching Update reference genome in depth plots Fix code path in EvidenceQc when run_ploidy is false Bug fix missing sample ID in median coverage Enable passing a threshold to govern the window for detection of dispersed deletions Handle zero-length arrays in JoinRawCalls sv-shell (WDL-independent pipeline-in-progress) WDL-independent version of GatherSampleEvidence Log stdout and stderr of tasks in sv_shell Implement a bash version of the Evidence QC workflow CI/CD Disable automated sv-shell and scramble docker updates temporarily while addressing R package installation issues Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v1.0.5...v1.1
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6931742510
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