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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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Update gatk_docker with CPX annotation changes to SVAnnotate
#632
epiercehoffman
closed
5 months ago
0
Remove CHR2 and END2 from INS in CleanVcf
#631
epiercehoffman
closed
5 months ago
1
Disable MakeCohortVcfMetrics by default to avoid pesky resource errors
#630
epiercehoffman
closed
5 months ago
0
Move cloud_sdk_docker to broad-dsde-methods
#629
mwalker174
closed
5 months ago
1
Release AoU filtering model
#628
mwalker174
closed
8 months ago
0
Update BEDTools version to 2.31.0
#627
VJalili
closed
8 months ago
2
Integrate ReshardVcf into ResolveComplexVariants
#626
mwalker174
closed
3 months ago
0
Find CN field for mCNVs in MainVcfQc without hard-coding order of format fields
#625
epiercehoffman
closed
9 months ago
0
WhamG memory issues hard to treat
#624
MattWellie
closed
9 months ago
2
Reduce SVConcordance memory usage
#623
mwalker174
closed
8 months ago
0
Change Vapor bed preprocessing errors to warnings
#622
mwalker174
closed
8 months ago
0
Modify WDL to Use N2 Machine Types for Enhanced Memory Allocation
#621
shadizaheri
closed
5 months ago
1
Make LocalizeReads Optional in GatherSampleEvidence
#620
kirtanav98
closed
9 months ago
0
Copy or move the files instead of creating symlinks in the LocalizeReads task for compatibility with CoA/TES.
#619
VJalili
closed
10 months ago
2
Rewrite the SplitVariants task command in TasksGenotypeBatch.wdl to call svtk only once
#618
kirtanav98
closed
9 months ago
0
Removed pairwise batch effect checks from WDL workflow
#617
shadizaheri
opened
11 months ago
0
Code crashing when running ResolveManta
#616
NahyunKong
closed
11 months ago
0
How can I apply downstream filtering steps to the cleaned VCF to further control the false discovery rate?
#615
elitefugua
opened
11 months ago
1
Reimplement ParseGenotypes in GenotypeComplexVariants
#614
mwalker174
closed
3 months ago
0
Add ReshardVcf workflow
#613
mwalker174
closed
10 months ago
0
Update cohort_mode_workspace_dashboard.md.tmpl
#612
kirtanav98
closed
11 months ago
0
Add extra information to dashboard with regards to which workflow versions should be run
#611
kirtanav98
closed
11 months ago
1
Reorganize docs on running the pipeline.
#610
VJalili
closed
4 months ago
2
Initial Python Version of Genotyping Script-Not Tested Yet
#609
shadizaheri
closed
5 months ago
1
Add Scramble docker to the build script & update docs
#608
VJalili
closed
11 months ago
0
Check for empty scatter in GenotypeDepthPart2
#607
epiercehoffman
closed
12 months ago
0
Can't find the vcf_stats file（MergeVcfWideStats.merged_bed_file）, how to generate it?
#606
jingydz
opened
12 months ago
1
Setup automatic updates to WDLs on Dockstore
#605
VJalili
closed
10 months ago
2
Update FilterOutlierSamples vcf attribute
#604
knathamuni
closed
4 months ago
1
Optimize Scramble
#603
mwalker174
closed
1 year ago
1
Make the Cromwell root config in the MELT workflow portable
#602
VJalili
closed
11 months ago
1
Update manta to 1.6.0
#601
mwalker174
closed
1 year ago
1
Toggle Collect PESR/Counts in GatherSampleEvidence with booleans
#600
epiercehoffman
closed
1 year ago
0
Fix allosomes_list bug
#599
MattWellie
closed
1 year ago
0
FilterGenotypes relies on unavailable tool
#598
MattWellie
closed
3 months ago
1
Updating Terra instructions in Workplace setup for removing data
#597
knathamuni
closed
4 months ago
1
Correct use of optimize_vcf_records_per_shard in FilterGenotypes
#596
mwalker174
closed
1 year ago
0
Fix melt insert size input type in EvidenceQC
#595
mwalker174
closed
1 year ago
0
Remove hgdp_1kgp_ped test batch input from MainVcfQc template
#594
mwalker174
closed
1 year ago
0
Make genome_tracks optional in FilterGenotypes
#593
MattWellie
closed
1 year ago
2
Update melt docker image to current latest build.
#592
VJalili
closed
1 year ago
1
Remove redundant GetPed task in GatherBatchEvidence.CNMOPS
#591
kirtanav98
closed
1 year ago
0
Filter mCNVs under 5kbp
#590
mwalker174
closed
1 year ago
0
Missing Script in Variant Resolution?
#589
MattWellie
closed
1 year ago
0
Update JoinRawCalls formatter arg in template
#588
mwalker174
closed
1 year ago
0
PED file validation
#587
epiercehoffman
closed
1 year ago
1
Make Vapor plots optional to store
#586
epiercehoffman
closed
1 month ago
1
Make LocalizeReads optional
#585
mwalker174
closed
8 months ago
1
Genotype filtering training labels and cutoff optimization
#584
mwalker174
closed
5 months ago
1
Remove CHR2 and END2 for CPX at the end of CleanVcf
#583
epiercehoffman
closed
1 year ago
0
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