Commits

History for

Commits on Jun 4, 2024

Permutect dataset engine outputs contig and read group indices, not names (broadinstitute#8860 )
davidbenjamin
authored
Mutect2 WDL and GetSampleName can handle multiple sample names in BAM headers (broadinstitute#8859 )
davidbenjamin
authored

Commits on Jun 3, 2024

Mutect2 germline resource can have split multiallelic format (broadinstitute#8837 )
davidbenjamin
authored
[BIOIN-1570] Fixed edge case in variant annotation (broadinstitute#8810 )
ilyasoifer
authored

Commits on May 17, 2024

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

Commits on May 15, 2024

VariantFiltration: added arg to write custom mask filter description in VCF header (broadinstitute#8831 )
meganshand
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 (broadinstitute#8759 )

nalinigans
and
Nalini Ganapati
authored

Commits on May 2, 2024

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

Commits on May 1, 2024

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

ldgauthier
and
jonn-smith
authored

Commits on Apr 18, 2024

Gc getpipeupsummaries use mappingqualityreadfilter (broadinstitute#8781 )
gokalpcelik
authored

Commits on Apr 12, 2024

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

Commits on Apr 11, 2024

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

Commits on Apr 10, 2024

Several GQ0 cleanup changes: (broadinstitute#8741 )
ldgauthier
authored

Commits on Apr 4, 2024

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

ilyasoifer
and
Dror Kessler
authored

Commits on Apr 1, 2024

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

Commits on Mar 25, 2024

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

Commits on Mar 12, 2024

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

Commits on Mar 7, 2024

fix no data hom refs (broadinstitute#8715 )
ldgauthier
authored

Commits on Feb 15, 2024

Handle CTX_INV subtype in SVAnnotate (broadinstitute#8693 )
epiercehoffman
authored

Commits on Feb 7, 2024

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

Commits on Jan 30, 2024

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

Commits on Jan 26, 2024

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

Commits on Jan 23, 2024

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

Commits on Dec 14, 2023

Commits on Dec 13, 2023

Update to htsjdk 4.1.0 (broadinstitute#8620 )
lbergelson
authored

Commits on Dec 12, 2023

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

Commits on Dec 11, 2023

Support for custom ploidy regions in HaplotypeCaller (broadinstitute#8609 )

authored

Commits on Dec 8, 2023

Update dependencies to address security vulnerabilities, and add a security scanner to build.gradle (broadinstitute#8607 )
droazen
authored