Somatic

How to recover a mutation from secondary alignment
- Laurent MANCHON
- February 01, 2023 08:41
0 votes 0 comments
Is it ok to use -L for each chromosome separately when running Mutect2?
- Xuning Wang
- January 30, 2023 21:41
0 votes 0 comments
Asking for advice on Mutect2 calling in somatic but amplicon data
- yangjw
- January 30, 2023 07:32
- Edited
0 votes 0 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
GatherVCFs error - provider not installed
- kvn95ss
- December 02, 2022 10:19
0 votes 1 comment
In case there is no vcf file from genome project, is it still possible to use the GetPileupSummaries?
- Arye Harel
- November 15, 2022 15:54
- Edited
0 votes 4 comments
af-only-gnomad.vcf.gz
- Shivangi Agarwal
- November 07, 2022 22:36
0 votes 1 comment
Could not find vcf.stats file after Mutect2
- Seke Keretsu
- November 02, 2022 01:15
0 votes 2 comments
Panel of Normals - inconsistent filtering behavior
- Paula Berry
- October 18, 2022 16:22
- Edited
0 votes 4 comments
Create Panel of Normals Issue
- Yuwei Bao
- October 12, 2022 00:51
0 votes 2 comments
Can Mutect2 calls tumor sample specific SNV under joint calling mode?
- Duo Xie
- August 31, 2022 23:34
- Edited
0 votes 3 comments
Diferencia entre varinates detectadas usando gatk 4.1.8.1 y 4.1.9.0
- Nefté Yañez
- August 29, 2022 07:23
0 votes 1 comment
Issue when running BaseRecalibrator
- Duo Xie
- August 20, 2022 16:16
0 votes 5 comments
GATK4 Somatic CNV - proportional coverage calculation blunted
- Kevin Meli
- August 17, 2022 20:30
0 votes 1 comment
Issue with MergeBamAlignment
- Javier
- July 21, 2022 19:28
0 votes 0 comments
Funcotator maf has different alt allele than vcf for some variants
- Balthasar
- July 11, 2022 11:34
1 vote 1 comment
Funcotator Custom Annotation Table Not Working
- Etienne Mahe
- July 04, 2022 01:39
0 votes 4 comments
Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz
- Saya Rene Dennis
- April 27, 2022 22:37
0 votes 3 comments
How to create Panel of Normals?
- Tanay Biswas
- March 25, 2022 13:16
- Edited
0 votes 7 comments
Mutect2 missing a low AF known deletion
- yingchen69
- January 12, 2022 16:50
0 votes 4 comments
Mutect stats table not found.
- Olena Maiakovska
- November 25, 2021 15:05
- Edited
0 votes 1 comment
GGA-mode gives PASS tag while the site failed in the normal workflow
- xiucz
- November 16, 2021 03:22
- Edited
0 votes 13 comments
Mutect2 bamout reports fewer reference reads than original bam, causing false positive call.
- CYWang
- October 03, 2021 11:30
0 votes 7 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.