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broadinstitute
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gatk-sv
A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Fix SplitVariants task in TasksGenotypeBatch.wdl to be compatible with downstream analysis
#647
kirtanav98
closed
4 months ago
0
Remove KING and PLINK
#646
mwalker174
closed
2 months ago
1
Replace `sv_pipeline_rdtest_docker` with `sv_pipeline_docker`.
#645
VJalili
closed
2 months ago
1
fix: add sd_locs_vcf_index input to SDtoBAF
#644
simojoe
opened
4 months ago
1
task SDtoBAF calls SiteDepthtoBAF without passing required index file
#643
simojoe
opened
4 months ago
0
SplitVariants task in TasksGenotypeBatch.wdl not compatible with downstream analysis
#642
leqi0001
closed
4 months ago
2
Add a preview version of the de-novo pipeline
#641
VJalili
closed
2 months ago
1
Update docs on building and hosting Docker images
#640
VJalili
closed
3 weeks ago
1
Replace `sv_pipeline_updates_docker` with `sv_pipeline_docker`
#639
VJalili
closed
2 months ago
0
Replace `sv_pipeline_hail_docker` with `sv_pipeline_docker`
#638
VJalili
closed
2 months ago
1
Make the ploidy table output a necessary output instead of an intermediate …
#637
kirtanav98
closed
4 months ago
0
Make the ploidy_table output a final output in JoinRawCalls
#636
kirtanav98
closed
1 month ago
1
Make manta region bed index required
#635
VJalili
closed
5 months ago
1
Replace `sv_pipeline_base_docker` with `sv_pipeline_docker`
#634
VJalili
closed
5 months ago
1
Change default behavior of GatherSampleEvidence to skip running module metrics
#633
VJalili
opened
5 months ago
3
Update gatk_docker with CPX annotation changes to SVAnnotate
#632
epiercehoffman
closed
2 months ago
0
Remove CHR2 and END2 from INS in CleanVcf
#631
epiercehoffman
closed
2 months ago
1
Disable MakeCohortVcfMetrics by default to avoid pesky resource errors
#630
epiercehoffman
closed
2 months ago
0
Move cloud_sdk_docker to broad-dsde-methods
#629
mwalker174
closed
2 months ago
1
Release AoU filtering model
#628
mwalker174
closed
5 months ago
0
Update BEDTools version to 2.31.0
#627
VJalili
closed
5 months ago
2
Integrate ReshardVcf into ResolveComplexVariants
#626
mwalker174
closed
1 week ago
0
Find CN field for mCNVs in MainVcfQc without hard-coding order of format fields
#625
epiercehoffman
closed
6 months ago
0
WhamG memory issues hard to treat
#624
MattWellie
closed
6 months ago
2
Reduce SVConcordance memory usage
#623
mwalker174
closed
5 months ago
0
Change Vapor bed preprocessing errors to warnings
#622
mwalker174
closed
5 months ago
0
Modify WDL to Use N2 Machine Types for Enhanced Memory Allocation
#621
shadizaheri
closed
2 months ago
1
Make LocalizeReads Optional in GatherSampleEvidence
#620
kirtanav98
closed
6 months ago
0
Copy or move the files instead of creating symlinks in the LocalizeReads task for compatibility with CoA/TES.
#619
VJalili
closed
7 months ago
2
Rewrite the SplitVariants task command in TasksGenotypeBatch.wdl to call svtk only once
#618
kirtanav98
closed
6 months ago
0
Removed pairwise batch effect checks from WDL workflow
#617
shadizaheri
opened
8 months ago
0
Code crashing when running ResolveManta
#616
NahyunKong
closed
8 months ago
0
How can I apply downstream filtering steps to the cleaned VCF to further control the false discovery rate?
#615
elitefugua
opened
8 months ago
1
Reimplement ParseGenotypes in GenotypeComplexVariants
#614
mwalker174
closed
1 week ago
0
Add ReshardVcf workflow
#613
mwalker174
closed
7 months ago
0
Update cohort_mode_workspace_dashboard.md.tmpl
#612
kirtanav98
closed
8 months ago
0
Add extra information to dashboard with regards to which workflow versions should be run
#611
kirtanav98
closed
8 months ago
1
Reorganize docs on running the pipeline.
#610
VJalili
closed
1 month ago
2
Initial Python Version of Genotyping Script-Not Tested Yet
#609
shadizaheri
closed
2 months ago
1
Add Scramble docker to the build script & update docs
#608
VJalili
closed
8 months ago
0
Check for empty scatter in GenotypeDepthPart2
#607
epiercehoffman
closed
9 months ago
0
Can't find the vcf_stats file(MergeVcfWideStats.merged_bed_file), how to generate it?
#606
jingydz
opened
9 months ago
1
Setup automatic updates to WDLs on Dockstore
#605
VJalili
closed
7 months ago
2
Update FilterOutlierSamples vcf attribute
#604
knathamuni
closed
1 month ago
1
Optimize Scramble
#603
mwalker174
closed
9 months ago
1
Make the Cromwell root config in the MELT workflow portable
#602
VJalili
closed
8 months ago
1
Update manta to 1.6.0
#601
mwalker174
closed
9 months ago
1
Toggle Collect PESR/Counts in GatherSampleEvidence with booleans
#600
epiercehoffman
closed
10 months ago
0
Fix allosomes_list bug
#599
MattWellie
closed
9 months ago
0
FilterGenotypes relies on unavailable tool
#598
MattWellie
closed
2 weeks ago
1
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