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1,210 Open 3,337 Closed
1,210 Open 3,337 Closed
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Issues list

Haplotypecaller error
#8984 opened Sep 18, 2024 by polymerase2010
2
How to filter on funcotation subfields
#8983 opened Sep 17, 2024 by keenhl
LeftAlignIndels Alignments added out of order issue when reads are fed in coordinate sorted order.
#8975 opened Sep 9, 2024 by gokalpcelik
gVCF ALT Column Showing Only <NON_REF>
#8974 opened Sep 9, 2024 by kotchanipar
GenotypeGVCFs error in GATK 4.6.0.0: java.lang.RuntimeException: Invalid deflate block found.
#8969 opened Sep 3, 2024 by hxtjc
WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
#8966 opened Aug 28, 2024 by ChrisSteel-bio
Strange output by Funcotator
#8965 opened Aug 27, 2024 by gevro
2
VariantFiltration failed
#8964 opened Aug 27, 2024 by Wasya-the-Wolf
2
Funcotator: all Clinvar fields blank
#8963 opened Aug 26, 2024 by gevro
3
HaplotypeCallerSpark Failed because GenotypesCache thrown NPE
#8961 opened Aug 23, 2024 by Xuehai-Chen
2
alt allels error
#8953 opened Aug 14, 2024 by gaochenx
1
Convergence Error running GATK GermlineCNVCaller cohort mode
#8952 opened Aug 14, 2024 by snakesch
5
SortSamSpark Required array length is too large
#8949 opened Aug 11, 2024 by fo40225
2 tasks
5
HaplotypeCaller is reporting DP in HOMREF region differently when ploidy is set to 1 with different Interval inputs bug HaplotypeCaller
#8943 opened Aug 6, 2024 by gokalpcelik
@jamesemery
6
301 tests fail, 37 are skipped
#8940 opened Aug 4, 2024 by yurivict
Tests fail to find libgkl libraries in /usr/local/lib
#8939 opened Aug 4, 2024 by yurivict
GermlineCNVCaller - python exited with 2
#8938 opened Aug 4, 2024 by lovelycatZ
1
Tests should print per-test status, otherwise it is difficult to see what tests fail or are skipped
#8937 opened Aug 2, 2024 by yurivict
GenotypeGVCFs memory issues on GATK 4.6.0.0
#8918 opened Jul 17, 2024 by jin0008
12
CreateSomaticPanelOfNormals: multiallelic sites wrongly added to PON despite --min-sample-count set to total input samples
#8916 opened Jul 17, 2024 by juliawiggeshoff
gatk Funcotator error
#8913 opened Jul 12, 2024 by l-magnificence
1
Problem with PathSeqPipelineSpark : Not generating bam
#8909 opened Jul 11, 2024 by martitroiani
Follow up on CNN deprecation done in the update to python 3.10.
#8907 opened Jul 9, 2024 by samuelklee
@droazen @samuelklee
2
Funcotator gnomAD incoherent number of output fields
#8858 opened Jun 3, 2024 by gokalpcelik
@jonn-smith
Docker container should allow use by non-privileged user
#8856 opened Jun 3, 2024 by potter-s
1 task
2
ProTip! no:milestone will show everything without a milestone.