Rc vs 1365 hatcher testing parquet#8845

Draft

RoriCremer wants to merge 42 commits intoah_var_storefrom

rc-vs-1365-hatcher_testing_parquet

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 Dec 14, 2023

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 12, 2024

Commits on Mar 19, 2024

non-compatible tweaks to ingestion to write our parquet files
koncheto-broad
committed

Commits on Jun 26, 2024

add reference and header parquet writers
RoriCremer
committed