broadinstitute gatk-sv issues

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing

BSD 3-Clause "New" or "Revised" License

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issues

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MELT Dockerfile

#697 c2997108 opened 4 hours ago
0
Update gatk docker with changes to handle CPX_TYPE for CTX

#696 epiercehoffman closed 2 days ago
0
Add genotype filtering Terra workflow configs and documentation

#695 mwalker174 opened 2 days ago
0
RdTest does not plot variants for which all samples are carriers

#694 epiercehoffman opened 6 days ago
0
Reduce memory usage in GenotypeSRPart1

#693 mwalker174 opened 1 week ago
0
Making the Vapor plots optional to store as a final output

#692 kirtanav98 closed 1 day ago
0
Trigger WDL tests on changes to /inputs and fix Terra config tests

#691 mwalker174 closed 2 weeks ago
0
Incorrect mCNV genotype counts in MainVcfQc

#690 mwalker174 opened 3 weeks ago
0
Deprecate single-batch Terra configs

#689 epiercehoffman closed 3 weeks ago
0
6F adjustment metadata matrices

#688 Dagsbio opened 4 weeks ago
3
Grouped MEI's with insertions in splitvariants.py

#687 kirtanav98 closed 2 days ago
0
Add NonZeroReferenceLengthAlignmentReadFilter read filter to CollectSVEvidence

#686 mwalker174 closed 4 weeks ago
0
Update docs on building inputs

#685 VJalili closed 3 weeks ago
1
Prevent sample ID mangling in WGD computation

#684 CuriousTim closed 1 month ago
4
X gets added to some sample IDs in WGD in EvidenceQc

#683 epiercehoffman closed 1 month ago
0
Set the default disk size in AnnotateIntervals as a function of input files size

#682 VJalili closed 1 month ago
0
Update GatherSampleEvidence & TrainGCNV docs

#681 VJalili opened 1 month ago
0
Extend the list supported syntax-highlighting languages

#680 VJalili closed 1 month ago
0
Update Docusaurus and its dependencies to v3.3.2.

#679 VJalili closed 1 month ago
0
Add support for annotating external AF from multiple datasets

#678 epiercehoffman opened 1 month ago
0
gCNV JointSegmentation fails on sex aneuploidies

#677 MattWellie closed 3 weeks ago
2
keep unresloved manta SVs and cluster them

#676 xuefzhao opened 1 month ago
0
Add documentation for the de-novo pipeline

#675 VJalili opened 1 month ago
0
Fix UnboundLocalError

#674 CuriousTim closed 1 month ago
0
UnboundLocalError in src/sv-pipeline/scripts/make_evidence_qc_table.py

#673 CuriousTim closed 1 month ago
1
Terra dashboard updates

#672 epiercehoffman closed 1 month ago
0
Make per-sample QC plots optional in MainVcfQc

#671 epiercehoffman closed 1 month ago
0
Update gnomad-v2 sample-level benchmarking data path

#670 epiercehoffman closed 1 month ago
0
Trivial change to sv-pipeline-virtual-env

#669 mwalker174 closed 2 months ago
0
Refactor workflow inputs/output for consistency

#668 VJalili opened 2 months ago
0
MEI to be calculated in MainVcfQc

#667 xuefzhao opened 2 months ago
1
Two small bugfixes to 02-EvidenceQC

#666 RCollins13 closed 2 months ago
0
Make MELT scripts independent of the execution path.

#665 VJalili closed 2 months ago
1
CPX_TYPE for CTX

#664 epiercehoffman closed 2 days ago
0
AD values in Annotation aren't Integers

#663 MattWellie opened 3 months ago
0
Scripts to create downsampled files

#662 VJalili opened 3 months ago
0
Integer-conformant AF values

#661 MattWellie closed 1 month ago
8
Annotate GD region overlap in AnnotateVcf

#660 epiercehoffman opened 3 months ago
0
svtk vcfcluster creates lists of INFO values when Number = 1

#659 epiercehoffman opened 3 months ago
1
Filter allosomal genotypes for samples with unassigned sex

#658 mwalker174 opened 3 months ago
0
Fix --par arg to compute_AFs.py in ShardedAnnotateVcf

#657 epiercehoffman closed 1 month ago
0
ImportError: dlopen: cannot load any more object with static TLS

#656 jingydz opened 3 months ago
1
Xz fixes 5

#655 xuefzhao closed 3 weeks ago
1
Remove outliers across per-contig VCFs

#654 epiercehoffman opened 3 months ago
0
Workflow to apply NCR and reference artifact filters and remove zero-carrier sites

#653 epiercehoffman opened 3 months ago
1
ScramblePart1 139 error code

#652 MattWellie opened 4 months ago
1
Modification of parameters

#651 andrewruttenberg opened 4 months ago
1
Make SplitVariants task in TasksGenotypeBatch.wdl compatible with downstream analysis

#650 kirtanav98 closed 4 months ago
0
MEIs in SplitVariants

#649 epiercehoffman opened 4 months ago
1
Look into higher than expected numbers of large CPX events

#648 epiercehoffman opened 4 months ago
0