Gg foo#9279

Draft

gbggrant wants to merge 180 commits intoEchoCallsetfrom

Commits on Feb 27, 2024

add link to README (#8705)
rsasch
authored
Added a note to AoU documentation describing possible need for more memory or disk on certain task. (#8704)
gbggrant
authored

Commits on Mar 1, 2024

Knit GvsExtractCohortFromSampleNames.wdl into GvsCalculatePrecisionAndSensitivity.wdl [VS-1245] (#8707)
rsasch
authored

Commits on Mar 5, 2024

add recommendation for dataset location in GCS (#8713)
rsasch
authored

Commits on Mar 7, 2024

Fix small typo [VS-1224] (#8720)
rsasch
authored

Commits on Mar 13, 2024

Fix bug in GvsBulkIngestGenomes.wdl (duplicate input!!) (#8736)
gbggrant
authored

Commits on Mar 18, 2024

VS-623 Exclude AS_YNG from Extract VCF (#8738)
gbggrant
authored

Commits on Mar 19, 2024

Updated changelog file for Beta release to include removal of AS_YNG field from VCFs. (#8743)
gbggrant
authored

Commits on Mar 22, 2024

Commits on Apr 1, 2024

VS-1190 Changes needed to support new Nirvana reference disk. (#8746)
gbggrant
authored

Commits on Apr 2, 2024

PGEN retry with more memory [VS-1314] (#8754)
mcovarr
authored

Commits on Apr 4, 2024

Docs for monitoring quotas and requesting increases [VS-1320] (#8760)
rsasch
authored

Commits on Apr 5, 2024

Use `noAddress` to limit use of external IPs [VS-1323] (#8764)
mcovarr
authored

Commits on Apr 8, 2024

Make CreateTables volatile [VS-1328] (#8765)
rsasch
authored

Commits on Apr 17, 2024

PGEN / VCF tieout [VS-1311] (#8779)
mcovarr
authored

Commits on Apr 19, 2024

Docker image ID in tags [VS-1340] (#8783)
mcovarr
authored

Commits on Apr 23, 2024

Commits on Apr 24, 2024

PLINK2 Docker [VS-1315] (#8792)
mcovarr
authored

Commits on Apr 26, 2024

VS-1310 Optionally convert filtered genotypes to no-calls (#8793)
gbggrant
authored

Commits on May 6, 2024

Commits on May 7, 2024

Commits on May 8, 2024

Commits on May 9, 2024

PGEN non-bonkers default disk size [VS-1279]
mcovarr
authored

Commits on May 10, 2024

Commits on May 13, 2024

VS-1368 The tarball is too damn big (#8829)

gbggrant
and
mcovarr
authored

Commits on May 15, 2024

Commits on May 16, 2024

Scatter adjustments [VS-516] (#8835)
mcovarr
authored

Commits on May 17, 2024

Support > 100 vet tables [VS-1377] (#8839)
mcovarr
authored

Commits on May 24, 2024

VS-1397 Update Tests - ah_var_store edition (#8846)
gbggrant
authored

Commits on May 30, 2024

bq query audit [VS-1396] (#8847)
mcovarr
authored

Commits on May 31, 2024

Clarify and set default for interval_list input [VS-1391] (#8853)
rsasch
authored

Commits on Jun 6, 2024

VS-430 Remove YNG status from vds (#8861)
gbggrant
authored

Commits on Jun 10, 2024

VS-1395 Have create vat from vds optionally take sites only vcf (#8851)
gbggrant
authored

Commits on Jun 17, 2024

Commits on Jun 18, 2024

VS-1413 Fix pgen merge chrom encoding (#8875)
gbggrant
authored

Commits on Jun 21, 2024

Some UI Improvements for GvsCreateVATfromVDS.wdl (#8881)
gbggrant
authored

Commits on Jun 24, 2024

Release new version of GVS (#8883)
rsasch
authored

Commits on Jun 28, 2024

Kd GVS GP self service doc updates (#8886)
kbergin
authored

Commits on Jul 10, 2024

Changes after first large pgen extract [VS-1332] (#8906)
rsasch
authored

Commits on Jul 15, 2024

VS-1433 add vcf validator to tests (#8903)
gbggrant
authored

Commits on Jul 18, 2024

Update GVS Docs to cover additional use cases and troubleshooting suggestions (#8917)

kbergin
and
mcovarr
authored

Commits on Jul 19, 2024

Put PGEN deliverable (instead of intermediate) files in output_gcs_dir [VS-431] (#8919)
rsasch
authored

Commits on Jul 22, 2024

Add integration test for BGE samples [VS-1225] (#8920)
rsasch
authored

Commits on Jul 23, 2024

Commits on Aug 1, 2024

Commits on Aug 5, 2024

VS-1461 Instructions to create vid to mapping table (#8932)
gbggrant
authored

Commits on Aug 6, 2024

ACAF updates [VS-1109] [VS-1366] (#8941)
mcovarr
authored

Commits on Aug 8, 2024

Don't Copy PGEN Interval Lists to Output Directory (#8946)
rsasch
authored

Commits on Aug 14, 2024

Update Script to Handle Both Files and FOFN [VS-1441] (#8954)
rsasch
authored

Commits on Aug 16, 2024

VS-1113 Update VQSR and VETS naming (#8948)
gbggrant
authored

Commits on Aug 19, 2024

Slight AoU docs adjustment [VS-1366] (#8955)
mcovarr
authored

Commits on Aug 21, 2024

VS-1470 Have Extract Cohort to PGEN write to cost_observability table (#8958)
gbggrant
authored

Commits on Aug 28, 2024

VS-1466 restructure export vcf for copy reasons (#8960)
gbggrant
authored

Commits on Sep 9, 2024

Commits on Sep 11, 2024

Update Docs Around Callset Cleanup and Cost [VS-1107] (#8976)
rsasch
authored

Commits on Sep 13, 2024

Tweak extract values based on Echo Runs [VS-1432] (#8979)
rsasch
authored

Commits on Sep 16, 2024

update cleanup doc (#8981)
rsasch
authored

Commits on Sep 24, 2024

Change Batch Size Parameter to Scatter Width For Ingest [VS-1218] (#8985)
rsasch
authored

Commits on Sep 27, 2024

Gg vs 1990 a widdle cleanup (#8970)
gbggrant
authored

Commits on Oct 1, 2024

VS-1422 Merge VAT changes in echo into ah_var_store (#8977)
gbggrant
authored

Commits on Oct 19, 2024

VS-1506 - Pull changes from EchoCallset into ah_var_store branch (#8993)
gbggrant
authored

Commits on Oct 30, 2024

Commits on Nov 5, 2024

Base cohort extract scatter width on loaded sample count [VS-1513] (#9028)
mcovarr
authored

Commits on Nov 7, 2024

Vs 1416 modify ingest to correctly handle ploidy differences in dragen 3 7 8 samples (#8994)
koncheto-broad
authored

Commits on Nov 12, 2024

[no ticket] pass query_project instead (#9036)
Qi77Qi
authored

Commits on Nov 13, 2024

Commits on Nov 14, 2024

VS-1515 - Passing ploidy_table_name into GvsExtractCallset.wdl (#9044)
gbggrant
authored

Commits on Nov 15, 2024

Maximum alt alleles guardrail [VS-1530] (#9033)
mcovarr
authored

Commits on Nov 19, 2024

Prepare for release of GVS 0.6.1 / RWB Echo [VS-1500] (#9048)
mcovarr
authored

Commits on Nov 20, 2024

Update docs for moved script [VS-1490] (#9050)
mcovarr
authored

Commits on Nov 21, 2024

VS 1528 Update the sharding of the samples in the VAT creation to be dependent on the number of samples (#9039)
RoriCremer
authored

Commits on Nov 25, 2024

Commits on Dec 10, 2024

Extract Cohort optimizations [VS-493] [VS-1516] (#9055)
mcovarr
authored

Commits on Jan 2, 2025

Add a few additional failures to our notes doc (#8980)
RoriCremer
authored

Commits on Jan 6, 2025

GCP Batch-friendly Cromwell root detection [VS-1532] (#9069)
mcovarr
authored

Commits on Jan 13, 2025

Monitoring script changes for GCP Batch [VS-1550] (#9071)
mcovarr
authored

Commits on Jan 14, 2025

Commits on Jan 15, 2025

VS-1170 documentation updates (#9076)
gbggrant
authored

Commits on Jan 21, 2025

Update AoU doc for header ingest [VS-1210] (#9083)
mcovarr
authored

Commits on Jan 28, 2025

Ploidy for Foxtrot VDS [VS-1418] (#9082)
mcovarr
authored

Commits on Feb 3, 2025

VS-1549 Add VAT to integration tests (#9085)
gbggrant
authored

Commits on Feb 6, 2025

Commits on Feb 7, 2025

v4 all the GitHub action things [VS-1573] (#9091)
mcovarr
authored

Commits on Feb 10, 2025

Fix exomes bug for 200 < # samples < 400 [VS-1533] (#9092)
mcovarr
authored

Commits on Feb 20, 2025

Commits on Mar 3, 2025

VS-1584 build variants docker on m4 (#9099)
gbggrant
authored

Commits on Mar 4, 2025

Correct mis-mapping of chr 5 for RWB [VS-1605] (#9109)
mcovarr
authored

Commits on Mar 5, 2025

Commits on Mar 6, 2025

Addressed an edge case in ScoreVariantAnnotations that can occur when one variant type is not present in the input VCF. [VS-1609] (#9113)
mcovarr
authored

Commits on Mar 7, 2025

Updated changelog again (#9114)
koncheto-broad
authored

Commits on Mar 18, 2025

Extract memory footprint part I [VS-1590] (#9116)
mcovarr
authored

Commits on Mar 21, 2025

Extract avros for a VDS but only include the NEW samples that are in Foxtrot (#9105)
RoriCremer
authored

Commits on Mar 26, 2025

VS-1449 add reference string to vcf (#9124)
gbggrant
authored

Commits on Apr 14, 2025

Commits on Apr 17, 2025

Drop samples from VDS during merge and rescore [VS-1641] (#9147)
mcovarr
authored

Commits on Apr 23, 2025

VS-1178 merge master into ah var store again (#9135)

authored

Commits on Apr 24, 2025

VS-1457 Add VAT clinvar reverse complement (#9070)
RoriCremer
authored

Commits on May 5, 2025

VS-1648 make VAT integration test work on chr20 or all (#9162)
gbggrant
authored

Commits on May 8, 2025

Half-bad hetvars: one bad allele fails the genotype [VS-1615] [VS-1649] (#9149)
mcovarr
authored

Commits on May 9, 2025

VS-1654. Don't allow usage of legacy SQL. (#9166)
gbggrant
authored

Commits on May 12, 2025

Patch GQ0 genotypes to no-calls on merge [VS-1653]
mcovarr
authored

Commits on May 20, 2025

Upgrade to Hail 0.2.134 [VS-1660] (#9177)
mcovarr
authored

Commits on May 21, 2025

Add the Clinvar Review Status as a filter (#9134)

authored

Commits on May 22, 2025

More doc updates for Foxtrot [VS-1659] (#9182)
mcovarr
authored

Commits on May 27, 2025

Variants Docker base image update [VS-1665] (#9184)
mcovarr
authored

Commits on May 28, 2025

VS-1505 move vds validation (#9187)
gbggrant
authored

Commits on May 29, 2025

Commits on Jun 2, 2025

Commits on Jun 3, 2025

Specify --max-rows explicitly to not truncate to 100 [VS-1664] (#9197)
mcovarr
authored

Commits on Jun 5, 2025

VS-1236. Removed extra copy of vds_validation.py (#9199)
gbggrant
authored

Commits on Jun 6, 2025

Fix GATK jar building in integration test [VS-1672] (#9203)
mcovarr
authored

Commits on Jun 9, 2025

Prep for 0.6.3 release [VS-1670] (#9194)
mcovarr
authored

Commits on Jun 10, 2025

VS-1566 add MANE to vat (#9204)
gbggrant
authored

Commits on Jun 13, 2025

Echo Unmapped VID Investigation [VS-1671] (#9202)
mcovarr
authored

Commits on Jun 16, 2025

VS-1583 Update monitoring script. (#9207)
gbggrant
authored

Commits on Jun 17, 2025

VS-1388 verify sample count in alt allele table (#9210)
gbggrant
authored

Commits on Jun 23, 2025

AnVIL 3K inspired VAT improvements [VS-1676] (#9211)
mcovarr
authored

Commits on Jun 24, 2025

Initial CLAUDE.md [VS-1677] (#9209)
mcovarr
authored

Commits on Jun 30, 2025

VS-1657 - Adding new annotations to the sites-only VCF. (#9212)
gbggrant
authored

Commits on Jul 1, 2025

VS-1684 Don't fail on monitoring log format (#9217)
gbggrant
authored

Commits on Jul 2, 2025

Echo samples in Foxtrot [VS-1663] (#9215)
mcovarr
authored

Commits on Jul 10, 2025

Don't fail alt_allele population if sample counts don't match [VS-1628] (#9221)
mcovarr
authored

Commits on Jul 15, 2025

Commits on Jul 17, 2025

master merge 2025-07-16 [VS-1707] (#9230)
mcovarr
authored

Commits on Jul 21, 2025

Ignore weirdly named vets tables [VS-1711] (#9232)
mcovarr
authored

Commits on Jul 23, 2025

Increase Default Disk for MergeVCFs and Default Memory for SelectVariants tasks for FoxTrot Callset
gbggrant
authored

Commits on Jul 28, 2025

VS-1716. Have Extract check for the existence of ploidy table (#9236)
gbggrant
authored

Commits on Jul 29, 2025

Commits on Jul 30, 2025

VS-1509. Get WDL validation working again. (#9237)
gbggrant
authored

Commits on Aug 7, 2025

Commits on Aug 11, 2025

Fix more superpartition table name matches [VS-1631] (#9247)
mcovarr
authored

Commits on Aug 13, 2025

Commits on Aug 14, 2025

Fix ploidy compatibility with VDS `intermediate_resume_point` [VS-1633] (#9252)
mcovarr
authored

Commits on Aug 18, 2025

VDS merge & rescore changes for updated Cloud SDK [VS-1640]
mcovarr
authored

Commits on Aug 21, 2025

VS-1732. Update GvsCallsetStatistics.wdl to look for table gnomad_v3_sites in a new location (#9255)
gbggrant
authored

Commits on Aug 27, 2025

Commits on Aug 28, 2025

Fix Hail cluster leakage [VS-1730] (#9260)
mcovarr
authored

Commits on Sep 5, 2025

VS-1732. Modify Callset Statistics calculation to break up the chromosomes (#9259)
gbggrant
authored

Commits on Sep 10, 2025

VS-1738. Add the variant id to the pgen output files (#9263)
gbggrant
authored

Commits on Sep 12, 2025

Vs 1737 - Build resilience in WeightedSplitIntervals tool (#9264)
koncheto-broad
authored

Commits on Sep 15, 2025

VS-1644 Update n_chunks calculation for vat creation (#9265)
gbggrant
authored

Commits on Sep 23, 2025

Commits on Sep 25, 2025