Skip to content

Pull requests: broadinstitute/gatk-sv

New pull request New
28 Open 599 Closed
28 Open 599 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Implement gCNV case mode in sv-shell sv-shell SV-shell script or configuration add or update.
#895 opened Nov 21, 2025 by VJalili • Draft
1 of 2 tasks
New GenerateBatchMetrics workflow
#894 opened Nov 20, 2025 by mwalker174 Loading…
Add single-sample pipeline to sv-shell sv-shell SV-shell script or configuration add or update.
#887 opened Nov 13, 2025 by VJalili • Draft
Eliminate stochasticity in Median Coverage calculation enhancement New feature or request
#867 opened Sep 9, 2025 by kjaisingh Loading…
1
Remove outdated code and documentation related to evidence assessment
#859 opened Aug 22, 2025 by epiercehoffman Loading…
2
Improve RD testing to recover overlapped CNVs > 100 kbp methods
#851 opened Aug 4, 2025 by kjaisingh • Draft
@kjaisingh
Update RegenotypeCNVs.wdl GetRegenotype task
#839 opened Jul 10, 2025 by knathamuni Loading…
fix no EVIDENCE bug in stitch_fragmented_CNVs.sh (#818)
#821 opened Jun 9, 2025 by xiaoli0 Loading…
1
Update package versions in Docker images.
#816 opened May 27, 2025 by VJalili • Draft
3
Ignore sites with null GTs during de novo rate calculation
#810 opened May 9, 2025 by epiercehoffman Loading…
1
Localize all the needed files, no streaming
#806 opened May 1, 2025 by VJalili • Draft
1 of 4 tasks
Introduce methods for standardized callset evaluation methods
#804 opened Apr 25, 2025 by kjaisingh • Draft
@kjaisingh
Update VM spot pricing in monitoring analysis scripts
#765 opened Jan 6, 2025 by mwalker174 Loading…
1
Migrate CleanVcf into GATK optimization
#733 opened Oct 17, 2024 by kjaisingh • Draft
@kjaisingh
Add documentation for the de-novo pipeline
#675 opened May 13, 2024 by VJalili • Draft
2 tasks
12
Refactor workflow inputs/output for consistency
#668 opened Apr 25, 2024 by VJalili • Draft
2 tasks done
Scripts to create downsampled files
#662 opened Apr 2, 2024 by VJalili Loading…
4 tasks done
Remove outliers across per-contig VCFs
#654 opened Mar 11, 2024 by epiercehoffman • Draft
Workflow to apply NCR and reference artifact filters and remove zero-carrier sites
#653 opened Mar 8, 2024 by epiercehoffman • Draft
1
fix: add sd_locs_vcf_index input to SDtoBAF
#644 opened Feb 12, 2024 by simojoe Loading…
1
2
Change default behavior of GatherSampleEvidence to skip running module metrics
#633 opened Jan 31, 2024 by VJalili • Draft
4
Removed pairwise batch effect checks from WDL workflow
#617 opened Nov 9, 2023 by shadizaheri Loading…
4
Add TransferVcfAnnotations workflow
#533 opened May 11, 2023 by mwalker174 • Draft
Extend functionality for outlier sample exclusion workflow
#496 opened Feb 11, 2023 by RCollins13 Loading…
4
Add reclustering WDLs (do not merge)
#446 opened Oct 12, 2022 by mwalker174 • Draft
ProTip! Mix and match filters to narrow down what you’re looking for.