Somatic

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 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
GatherVCFs error - provider not installed
- kvn95ss
- December 02, 2022 10:19
0 votes 1 comment
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
GenomicsDBImport error: USER ERROR has occurred: Duplicate sample: 1. Sample was found in both file: Completed
- Yuna Son
- August 08, 2020 02:58
0 votes 12 comments
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
sample size for somatic CNV
- Muntadher Jihad
- December 02, 2022 12:04
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 creation error: GenomicsDBImport does not support GVCFs with MNPs Answered
- Ranjan J. Sarma
- November 02, 2022 07:06
- Edited
0 votes 1 comment
Can Mutect2 calls tumor sample specific SNV under joint calling mode?
- Duo Xie
- August 31, 2022 23:34
- Edited
0 votes 3 comments
af-only-gnomad.vcf.gz
- Shivangi Agarwal
- November 07, 2022 22:36
0 votes 1 comment
Panel of Normals - inconsistent filtering behavior
- Paula Berry
- October 18, 2022 16:22
- Edited
0 votes 4 comments
Error while running ModelSegments Answered
- onurerdoganmd
- November 09, 2021 20:52
0 votes 15 comments
Create Panel of Normals Issue
- Yuwei Bao
- October 12, 2022 00:51
0 votes 2 comments
Funcotator error: Only IGRs were produced for this dataset Answered
- Mina
- September 16, 2022 12:23
0 votes 4 comments
Mutect2 cannot generate stats file and f1r2.tar.gz file Answered
- Yi Huang
- September 21, 2022 07:26
0 votes 4 comments
GATK Muteck2 missing call Answered
- Marco Chiapello
- September 23, 2022 09:14
1 vote 2 comments
Picard error (AddOrReplaceReadGroups) Answered
- Hyesun Cho
- September 19, 2022 19:57
0 votes 4 comments
Issue when running BaseRecalibrator
- Duo Xie
- August 20, 2022 16:16
0 votes 5 comments
Increased number of false positives in Mutect2 GATK 4.1.7.0
- registered_user
- May 18, 2020 12:53
- Edited
0 votes 15 comments
improt gcnvkernel fails. somehting to do with theano lock Answered
- simon lee
- September 03, 2022 11:04
0 votes 3 comments
Difference between variants detected using gatk 4.1.8.1 and 4.1.9.0 Answered
- Nefté Yañez
- August 31, 2022 06:30
0 votes 2 comments
Mutect2 filter : clustered_events definition Answered
- whynot
- February 12, 2020 05:08
0 votes 7 comments

Welcome

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.