Somatic

The mutect ERROR：Please add an explicit type tag :NAME listing the correct type from among the supported types Answered
- 灵己孟
- June 28, 2021 03:15
0 votes 3 comments
Error while running CreateReadCountPanelOfNormals with gatk-4.1.4.1 Answered
- Alice Shen
- June 10, 2021 07:36
0 votes 3 comments
MuTect2 Mismatch between the reference haplotype and the reference assembly graph path. Answered
- Heejun Jang
- June 07, 2021 02:53
0 votes 1 comment
The output of Mutect2 cannot be accepted by FilterMutectCalls in GATK-4.2.0.0 Answered
- Qihan Long
- June 04, 2021 03:25
- Edited
0 votes 10 comments
The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered
- Ce Wang
- May 25, 2021 06:08
- Edited
0 votes 19 comments
How do I set less stringent germline filtering in Mutect2 / filtermutectcalls, many false negatives Answered
- Tjitske de Vries
- May 21, 2021 09:47
0 votes 1 comment
Mysterious Funcotator issue Answered
- Robert Bremel
- May 21, 2021 01:22
0 votes 8 comments
MergeBamAlignment produces unknown error Answered
- vctrymao
- May 18, 2021 16:19
- Edited
0 votes 4 comments
CollectAllelicCounts- Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded Answered
- rahelp
- May 16, 2021 13:17
0 votes 12 comments
IlluminaBasecallsToSam does not demultiplex NovaSeq barcoded reads Answered
- myourshaw
- May 10, 2021 21:46
- Edited
0 votes 5 comments
java.lang.OutofMemoryError: GC overhead limit exceeded Answered
- Jack Prazich
- May 03, 2021 16:54
0 votes 28 comments
GenomicsDBImport does not support GVCFs with MNPs Answered
- Rodolfo Adrián Arriaga Rivera
- April 23, 2021 16:52
- Edited
0 votes 1 comment
Mutect2
- Sotaro Kanematsu
- April 14, 2021 07:24
0 votes 1 comment
Badly formed genome unclippedLoc: Contig NC_007605 given as location, but this contig isn't present in the Fasta sequence dictionary Answered
- rahelp
- April 12, 2021 13:36
0 votes 7 comments
Why do a clear expected variant not show up in the Mutect2 vcf file Answered
- Nabeel Ahmed
- April 07, 2021 09:13
0 votes 14 comments
CreateSomaticPanelOfNormals ALT allele bug Answered
- G E
- April 02, 2021 15:19
- Edited
0 votes 10 comments
Funcotator data source not correct Answered
- Jamie Xie
- March 29, 2021 20:42
- Edited
0 votes 13 comments
Issue Regarding CNV_Somatic_Pair Workflow
- Hanbing Song
- March 23, 2021 00:02
0 votes 0 comments
Mutect2 failing to produce F1R2.tar.gz files on TCGA bam (tumor-normal pairs) Answered
- TMB
- March 10, 2021 17:29
0 votes 5 comments
Variant called in reads from ArtificialHaplotypeRG Answered
- yingchen69
- March 09, 2021 05:21
0 votes 4 comments
Picard CrosscheckFingerprint: Sequence dictionaries are not the same size Answered
- Doris Fu
- March 08, 2021 20:17
- Edited
0 votes 3 comments
FilterAlignmentArtifacts - only emitting PASS variants Answered
- GE
- March 01, 2021 15:38
0 votes 3 comments
Missing documentation on strict_strand Answered
- GE
- February 28, 2021 19:15
- Edited
0 votes 4 comments
strand_bias filtering is never emitted Answered
- GE
- February 28, 2021 18:11
- Edited
0 votes 7 comments
FilterMutectCalls didn't filtered any variants for my vcf file Answered
- Xiya Song
- February 28, 2021 11:02
0 votes 3 comments
Mutect2 - Joint calling Answered
- Yen-Ping Yeh
- February 23, 2021 08:44
0 votes 8 comments
HaplotypeCaller VCF for PON
- Steven Bentley
- February 22, 2021 23:05
0 votes 3 comments
1 year-old bug in libgkl that has not been fixed affecting FilterAlignmentArtifacts and HaplotypeCaller
- GE
- February 18, 2021 23:16
0 votes 3 comments
Bug: Badly formed genome unclippedLoc
- GE
- February 16, 2021 22:43
0 votes 12 comments
FilterMutectCalls --unique-alt-read-count argument
- Greg Goralogia
- February 16, 2021 20:48
0 votes 10 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.