[DRAFT] Merge master to ah var store again [VS-1178]#8890

Draft

mcovarr wants to merge 66 commits intoah_var_storefrom vs_1178_merge_master_to_ah_var_store_again

+295,751-286,530

Commits on Oct 11, 2023

Funcotator Update for Datasource Release V1.8 (#8512 )
jamesemery
authored
Fixed Funcotator VCF output renderer to correctly preserve B37 contig names on output for B37 aligned files (#8539 )
jamesemery
authored

Commits on Nov 3, 2023

Fix for events not in minimal representation (#8567 )
meganshand
authored

Commits on Nov 13, 2023

Commits on Nov 14, 2023

Update our HTSJDK dependency to 4.0.2 (#8584 )
droazen
authored

Commits on Nov 15, 2023

Update picard to 3.1.1 (#8585 )
lbergelson
authored

Commits on Nov 26, 2023

Add option to AnalyzeSaturationMutagenesis to keep disjoint mates (#8557 )
odcambc
authored

Commits on Nov 28, 2023

New/Updated Flow Based Read tools (#8579 )
dror27
authored

Commits on Dec 6, 2023

GroundTruthScorer doc update (#8597 )
dror27
authored

Commits on Dec 8, 2023

Commits on Dec 9, 2023

Commits on Dec 11, 2023

Commits on Dec 12, 2023

Update the GATK base image to a newer LTS ubuntu release (#8610 )
droazen
authored

Commits on Jan 23, 2024

Rewrite complex SV functional annotation in SVAnnotate (#8516 )
epiercehoffman
authored

Commits on Jan 26, 2024

Improvements to Mutect2's Permutect training data mode (#8663 )
davidbenjamin
authored

Commits on Jan 30, 2024

normal artifact lod is now defined without the extra minus sign (#8668 )
davidbenjamin
authored

Commits on Feb 7, 2024

Parameterize the logging frequency for ProgressLogger in GatherVcfsCloud. (#8662 )
gbggrant
authored

Commits on Feb 15, 2024

Handle CTX_INV subtype in SVAnnotate (#8693 )
epiercehoffman
authored

Commits on Mar 5, 2024

Move to GenomicsDB 1.5.2 which supports M1 macs (#8710 )
nalinigans
authored

Commits on Mar 7, 2024

Commits on Mar 8, 2024

Update the setup_cloud github action (#8651 )
lbergelson
authored

Commits on Mar 12, 2024

Fix to long deletions that overhang into the assembly window causing exceptions in HaplotypeCaller (#8731 )
jamesemery
authored

Commits on Mar 18, 2024

dragstr model in Mutect2 WDL (#8716 )
davidbenjamin
authored

Commits on Mar 19, 2024

Update README to include list of popular software included in docker image (#8745 )
rickymagner
authored

Commits on Mar 20, 2024

Now we should be excluding the test folder from code coverage calculations (#8744 )
KevinCLydon
authored

Commits on Mar 25, 2024

Make M2 haplotype and clustered events filters smarter about germline events (#8717 )
davidbenjamin
authored

Commits on Apr 1, 2024

Funcotator: suppress a log message about b37 contigs when not doing b37/hg19 conversion (#8758 )
droazen
authored

Commits on Apr 4, 2024

SNVQ recalibration tool added for flow based reads (#8697 )

ilyasoifer
and
Dror Kessler
authored

Commits on Apr 10, 2024

Several GQ0 cleanup changes: (#8741 )
ldgauthier
authored

Commits on Apr 11, 2024

Re-commit large files as lfs stubs (#8769 )
lbergelson
authored

Commits on Apr 12, 2024

Enable ReblockGVCF to subset AS annotations that aren't "raw" (pipe-delimited) (#8771 )
ldgauthier
authored

Commits on Apr 18, 2024

Gc getpipeupsummaries use mappingqualityreadfilter (#8781 )
gokalpcelik
authored

Commits on May 1, 2024

Add malaria spanning deletion exception regression test with fix (#8802 )

ldgauthier
and
jonn-smith
authored

Commits on May 2, 2024

Bug fix in flow allele filtering (#8775 )
ilyasoifer
authored

Commits on May 6, 2024

Allow for GT to be a nocall if GQ and PL[0] are zero instead of homref in GenomicsDB (#8759 )

nalinigans
and
Nalini Ganapati
authored

Commits on May 9, 2024

Reduced docker layers in GATK image from 44 to 16 (#8808 )
kevinpalis
authored

Commits on May 15, 2024

VariantFiltration: added arg to write custom mask filter description in VCF header (#8831 )
meganshand
authored

Commits on May 17, 2024

Bigger Permutect tensors and Permutect test datasets can be annotated with truth VCF (#8836 )
davidbenjamin
authored

Commits on Jun 3, 2024

Commits on Jun 4, 2024

Commits on Jun 13, 2024

Fixed a bug in AlleleFiltering that ignored more than a single sample (#8841 )
ilyasoifer
authored

Commits on Jun 24, 2024

Merge remote-tracking branch 'origin/ah_var_store' into vs_1178_merge_master_to_ah_var_store_again
mcovarr
committed