Other

No results of CollectvariantCallingMetrics Answered
- Yenan
- November 30, 2020 07:13
0 votes 30 comments
Panel of Normals Documentation Answered
- Ryan Gimple
- April 16, 2020 17:48
1 vote 16 comments
DepthofCoverage GATK4.1.7.0 -gene-list Answered
- marta r
- May 27, 2020 14:19
0 votes 15 comments
--tmp-dir option user error Answered
- Brynjar Sigurðsson
- August 10, 2020 12:22
0 votes 13 comments
CNNScoreVariants carshes with java.lang.NullPointerException Answered
- riederd
- January 17, 2020 15:29
1 vote 13 comments
Error in running GenomicsDBConfigException Answered
- Shivangi Agarwal
- December 20, 2021 14:51
0 votes 12 comments
GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered
- APato
- February 03, 2020 21:28
0 votes 10 comments
Call-caching not functional running cromwell locally on GCP VM Answered
- ibrahimkurt
- December 08, 2020 16:40
0 votes 9 comments
GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
- Nils Homer
- August 06, 2020 00:13
1 vote 9 comments
Can't explain the number of reads FilterSamReads outputs Answered
- Aki Jarl Laruson
- July 28, 2021 23:29
0 votes 8 comments
Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
- KATHIE NGO
- August 27, 2020 17:31
- Edited
0 votes 8 comments
SelectVariants v4.1.6.0 doesn't select the variants as expected Answered
- ABours
- June 02, 2020 13:26
0 votes 8 comments
Contamination calculation on single file don't detect contaminated samples Answered
- Vladislav Maximov
- October 14, 2021 15:03
0 votes 7 comments
DepthOfCoverage with -gene-list and readgroup as --partition-type options Answered
- David Jaspez
- May 06, 2021 14:58
0 votes 7 comments
ApplyBQSR no positional argument is defined for this tool Answered
- Jose Aragon
- March 06, 2021 14:26
0 votes 7 comments
Accessing the resource bundle. Answered
- nagam surya
- June 28, 2022 18:35
0 votes 6 comments
CNNScoreVariants Issues with environment and Java version Answered
- Kathrin B
- April 13, 2022 15:07
- Edited
0 votes 6 comments
Error in GenomicsDBImport: Invalid deflate block found Answered
- Lauren Hennelly
- February 26, 2022 20:26
1 vote 6 comments
GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source: Answered
- Morgan Sparks
- October 12, 2021 11:46
0 votes 6 comments
Truncated bam file after running ReplaceSamHeader(Picard) Answered
- kostas alexiou
- November 17, 2020 15:12
0 votes 6 comments
FindBadGenomicKmersSpark running indefinitely Answered
- Cher Wei Yuan
- August 02, 2022 02:25
0 votes 5 comments
Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character Answered
- Graeme Thorn
- May 27, 2022 21:05
- Edited
0 votes 5 comments
GC overhead limit exceeded using Mutect2 only tumor version Answered
- Shirliya Dadon
- February 09, 2022 12:53
- Edited
0 votes 5 comments
CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered
- rcorbett
- December 06, 2021 18:45
0 votes 5 comments
MarkduplicatesSpark failed Answered
- lid.zigh
- November 23, 2021 13:44
0 votes 5 comments
ShiftFasta creates empty intervals file Answered
- Ram
- October 21, 2022 07:56
- Edited
0 votes 4 comments
How can I build the GATK jar so that the intel native libraries are available? Answered
- Mark Schreiber
- September 22, 2022 16:49
0 votes 4 comments
libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered
- Marta Giovalli
- September 14, 2022 12:47
- Edited
0 votes 4 comments
Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
- pb
- July 13, 2022 14:15
0 votes 4 comments
Refseq accession number and version number in Funcotator Answered
- TMB
- April 26, 2022 04:13
0 votes 4 comments

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GATK Team Out of Office

The GATK team will be out of office during December 9th 2022 to January 9th 2022 in observance of the holidays. We will not be able to answer posts from within this period. If you are still experiencing issues when we are back, please re-post your inquiry.