Somatic

strand bias and orientation bias
- that girl
- December 02, 2020 06:51
5 votes 1 comment
Custom made Panel of Normals required?
- Pedro Miguel Raposo
- July 07, 2020 10:01
- Edited
2 votes 2 comments
Generating ACS like output from new GATK CNV pipeline (WGS)
- Jett Crowdis
- June 26, 2020 18:11
2 votes 4 comments
Funcotator maf has different alt allele than vcf for some variants
- Balthasar
- July 11, 2022 11:34
1 vote 1 comment
Funcotator Errors : I/O error in the advisory file locking logic (disk I/O error)
- Min-Hwan Sohn
- November 26, 2020 03:56
- Edited
1 vote 1 comment
How do I merge f1r2.tar.gz files when parallelizing Mutect2 pipeline?
- Jenifer
- October 28, 2020 17:25
- Edited
1 vote 1 comment
MarkDuplicatesSpark error missing Read Group fields
- Field -Ye Tian
- October 09, 2020 16:45
1 vote 1 comment
CalculateContamination "there is no such column: contig"
- Jensen Richardson
- July 05, 2020 18:02
1 vote 8 comments
gatk CollectAllelicCounts error
- peterchung
- May 26, 2020 03:23
- Edited
1 vote 6 comments
Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations
- Saba
- April 29, 2020 15:54
- Edited
1 vote 15 comments
Mutect2 - somatic variant calling with/without matched normal sample
- D B
- February 26, 2020 19:33
- Edited
1 vote 14 comments
MergeBamAlignment Error: ArrayIndexOutOfBoundsException
- Jared Jurss
- February 19, 2020 22:02
1 vote 3 comments
Problems combining gVCFs that have thousands of scaffolds
- Dch
- February 11, 2020 23:24
- Edited
1 vote 5 comments
Mutect2 variant calling output with tumor and matched normal: 0/1 in all variants called
- RicPin
- February 10, 2020 15:41
- Edited
1 vote 5 comments
Call germline mutations from Mutect2
- Chadi Saad
- January 14, 2020 10:30
1 vote 3 comments
Huge number of variants in tumor only mode as compared to T/N paired mode using Mutect2
- Shivangi Agarwal
- March 09, 2023 22:26
0 votes 3 comments
Somatic CNV Workflow Tutorials
- Yuwei Bao
- March 02, 2023 20:45
0 votes 1 comment
Mutect2 VCF out Tumor Normal
- Charitra K
- March 01, 2023 07:53
0 votes 5 comments
Strange differences in detected variants called by mutect2 --dont-use-soft-clipped-bases true vs false
- Jana Marie Schwarz
- February 22, 2023 16:26
0 votes 1 comment
How to recover a mutation from secondary alignment
- Laurent MANCHON
- February 01, 2023 08:41
0 votes 2 comments
Is it ok to use -L for each chromosome separately when running Mutect2?
- Xuning Wang
- January 30, 2023 21:41
0 votes 1 comment
Asking for advice on Mutect2 calling in somatic but amplicon data
- yangjw
- January 30, 2023 07:32
- Edited
0 votes 2 comments
How to call somatic variants without normal matched sample (cfDNA)
- Abel G
- January 26, 2023 11:45
0 votes 0 comments
Somatic mutations detection using mutect2
- Varun Gupta
- January 23, 2023 16:17
0 votes 0 comments
GatherPileupSummaries does not sort input variants
- Evan Wu
- January 20, 2023 23:00
0 votes 0 comments
Problem generating germline resource file for Mutect2
- Jaime Schwoch
- January 04, 2023 01:51
0 votes 0 comments
Mutect2 VCF sample order in tumor normal paired call
- Thomas Sunghoon Huh
- December 20, 2022 08:49
0 votes 0 comments
How do if remove Germline Variants from my variant calling file ?
- Seke Keretsu
- December 08, 2022 21:23
0 votes 0 comments
Error - Mutect2 PG tag
- A
- December 08, 2022 02:56
0 votes 0 comments
sample size for somatic CNV
- Muntadher Jihad
- December 02, 2022 12:04
0 votes 1 comment

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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.