broadinstitute/gatk

Issues

• install error for gatk-4.6.1.0

  #9115 opened a month ago by splaisan
  5

• when I use gatk to identify variants in a bam file converted from gam using vg surject, I get error

  #9119 opened a month ago by ChenDepp
  2

• PostprocessGermlineCNVCalls outputs wrong genotyped-segments results

  #9111 opened a month ago by DiabloRex
  0

• Hardcoded HTSJDK JEXL genotype filter bindings not working as expected for VariantFiltration.

  #9108 opened a month ago by gokalpcelik
  0

• GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message

  #9104 opened a month ago by Alipha-Clisa
  0

• GtfToBed errors out with `because "gene" is null`

  #9103 opened a month ago by mmahmoudian
  2

• Funcotator gnomAD google bucket unaccessible

  #9101 opened a month ago by zhanyinx
  3

• Efficiently perform simple merge/append on many VCFs?

  #9097 opened 2 months ago by bbimber
  4

• Docker 4.6.1.0 image not finding includes

  #9084 opened 2 months ago by pjgreer
  1

• Miscalling of SNPs and GQ value of 0

  #9086 opened 2 months ago by Sgornard
  9

• RevertSam collapses duplicate records and adds SA tag.

  #9090 opened 2 months ago by rajwanir
  4

• negative CNN_1D scores

  #9088 opened 2 months ago by MarionFresquet
  2

• macOS install

  #9074 opened 3 months ago by BenjaminDEMAILLE
  1

• Best Approach for Variant Calling with Mutect2 on Drug-Sensitive and Drug-Resistant Cancer Cell Lines

  #9081 opened 2 months ago by jenny8030
  3

• Enabling PDHMM causes GVCF mode to fail.

  #9041 opened 5 months ago by gokalpcelik
  1

• Help with interval list

  #9065 opened 3 months ago by vappiah
  2

• FilterAlignmentArtifacts - Padded span must contain active span

  #9075 opened 3 months ago by dansteiert
  0

• Homebrew

  #9073 opened 3 months ago by BenjaminDEMAILLE
  2

• KeyError in Post Process Germline Calls (Germline CNV Caller Workflow)

  #9072 opened 3 months ago by hkirmak
  2

• GenomicsDBImport and CombineGVCFs results don't match

  #9024 opened 3 months ago by gokalpcelik
  1

• Problem in gvcf interplay between clair3 and gatk

  #9068 opened 3 months ago by johannesgeibel
  1

• VariantAnnotator giving error "No overlapping contigs found"

  #9067 opened 3 months ago by khanshahan
  1

• Scorevariants python package not found when running NVScoreVariants

  #9066 opened 3 months ago by poconnel3
  1

• Variant annotator step in jointcalling procedure

  #9064 opened 3 months ago by SiddhiJani
  0

• java with conda install

  #9063 opened 4 months ago by stuartwillis
  0

• python exited with 1. Theano error.

  #9062 opened 4 months ago by lovelycatZ
  1

• GATK 4.6. SelectVariants not applying --select filters

  #9060 opened 4 months ago by FLsandell
  1

• Single-core job CPU efficiency above 100% on SLURM

  #9057 opened 4 months ago by dkioroglou
  4

• 'Cannot read non-existent file' issue related to incorrect parsing of paths

  #9038 opened 5 months ago by jphruska
  3

• FilterIntervals will get rid of Y chromosome intervals if there are >50% of female samples

  #9043 opened 5 months ago by NotAPoetButACriminal
  2

• Genotype Discrepancy Between Individual and Merged GVCF Files Using GATK

  #9030 opened 5 months ago by jiangluguang123
  0

• Issue Running GATK Mitochondrial Pipeline

  #9037 opened 5 months ago by jingxiant
  0

• PON filtering logic and tag in vcf.gz file

  #9035 opened 5 months ago by YuanTian1991
  0

• 0 or 1 based coordinates.

  #9029 opened 5 months ago by vappiah
  1

• Why is it possible to visualize a mutation at a specific locus in the BAM file in IGV, but cannot be called using mutect2?

  #9021 opened 5 months ago by Joyjoyjoyc
  0

• Memory leak in GenotypeGVCFs with `-all-sites`

  #8989 opened 6 months ago by brisk022
  8

• Add hap.py/som.py benchmarking results to docs for each release

  #9019 opened 5 months ago by skchronicles
  0

• Handling low bases in AD calculation

  #9014 opened 6 months ago by pogodina-nadezda
  1

• Potential Mismatch between the MAF output mode and VCF output mode on Gencode V43

  #9013 opened 6 months ago by jamesemery
  0

• Hook up the Python-based unit tests for NVScoreVariants to our test suite

  #9011 opened 6 months ago by droazen
  0

• Possible bug in GenotypeGVCFs 4.6.0.0, affecting all genotyping applications

  #9007 opened 6 months ago by gevro
  6

• SIGSEGV when running gatk/4.6.0.0

  #8988 opened 6 months ago by emwjacobson
  6

• Base-specific Phred score filtering/output options in AnalyzeSaturationMutagenesis

  #8995 opened 6 months ago by BenjaminWehnert1008
  1

• Feature Request: Progress Bar Estimated Time Remaining

  #8997 opened 6 months ago by jonn-smith
  0

• Update VariantRecalibrator RScript Compatibility with Newer ggplot2 Versions

  #8992 opened 6 months ago by Nanderson246
  1

• Haplotypecaller error

  #8984 opened 7 months ago by polymerase2010
  2

• How to filter on funcotation subfields

  #8983 opened 7 months ago by keenhl
  0

• gVCF ALT Column Showing Only <NON_REF>

  #8974 opened 7 months ago by kotchanipar
  0

• LeftAlignIndels Alignments added out of order issue when reads are fed in coordinate sorted order.

  #8975 opened 7 months ago by gokalpcelik
  0

• GenotypeGVCFs error in GATK 4.6.0.0: java.lang.RuntimeException: Invalid deflate block found.

  #8969 opened 7 months ago by hxtjc
  0