Somatic

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
GATK Muteck2 missing call Answered
- Marco Chiapello
- September 23, 2022 09:14
1 vote 2 comments
Mutect2 cannot generate stats file and f1r2.tar.gz file Answered
- Yi Huang
- September 21, 2022 07:26
0 votes 4 comments
Picard error (AddOrReplaceReadGroups) Answered
- Hyesun Cho
- September 19, 2022 19:57
0 votes 4 comments
Funcotator error: Only IGRs were produced for this dataset Answered
- Mina
- September 16, 2022 12:23
0 votes 4 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
GenotypeGVCFs Answered
- Yumi Hashi
- August 17, 2022 08:15
0 votes 1 comment
GATK4 ModelSegment Error Allelic-count sites must be identical across all samples Answered
- Linghao Song
- July 11, 2022 19:56
0 votes 2 comments
Combine two panel-of-normals files Answered
- Robin Mjelle
- July 08, 2022 12:03
0 votes 1 comment
Creating Panel of Normals (PoN) from Blood Sample of cancer patients Answered
- Ranjan J. Sarma
- July 05, 2022 08:15
- Edited
1 vote 9 comments
Panel of normal issue Answered
- Simon Haefliger
- June 29, 2022 08:04
0 votes 1 comment
Funcotator: Unable to open SQLite DB for COSMIC Answered
- AB
- June 03, 2022 19:23
- Edited
0 votes 7 comments
ModelSegments not reading allelic counts file Answered
- Ross Jackson
- May 11, 2022 06:36
0 votes 1 comment
ModelSegments - java.lang.IllegalArgumentException: Metadata of the allelic counts and the segments do not match Answered
- Tony Tan
- April 19, 2022 02:48
- Edited
0 votes 3 comments
Error in building panel of normal in somatic copy number variation calling Answered
- Lei Yu
- April 04, 2022 21:55
0 votes 4 comments
Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered
- zzh
- March 29, 2022 03:39
0 votes 5 comments
FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered
- Francesco Mazzarotto
- March 23, 2022 14:16
0 votes 9 comments
A USER ERROR has occurred: Duplicate sample: PD4086bv2. Sample was found in both file Answered
- jesus ix ballote
- March 04, 2022 20:34
0 votes 7 comments
In Mutect2 force-calling allele via --alleles does not force-call the allele Answered
- Rahul Gupta
- February 04, 2022 17:13
- Edited
0 votes 14 comments
FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered
- ElenaGrassi
- February 03, 2022 10:28
0 votes 9 comments
Read-orientation filter removes tens of thousands of somatic variants after FilterMutectCalls Answered
- Santiago Sanchez
- January 25, 2022 18:21
0 votes 6 comments
af-only-gnomad.raw.sites.b37.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file Answered
- linouhao
- January 19, 2022 02:05
0 votes 3 comments
Baserecalibarator error: half of the files worked without any error Answered
- Huma Shehwana
- January 17, 2022 12:19
0 votes 1 comment
Mutect2 unexpected false negative due to changes in smith-waterman parameters? Answered
- myourshaw
- January 14, 2022 20:14
- Edited
0 votes 3 comments
Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start Answered
- yqiu
- January 06, 2022 00:13
- Edited
1 vote 13 comments
mutect2.bam could not find the mutation, but bqsr found the mutation Answered
- cjz
- December 09, 2021 08:04
0 votes 1 comment
mutect2 genotyping wrong? Answered
- Jeffcgen2000
- December 02, 2021 22:54
0 votes 1 comment
How to decrease the likelihood threshold for a candidate haplotype to be called as a genotype in Mutect2 Answered
- Yussanne Ma
- November 19, 2021 02:58
0 votes 9 comments
Error while running ModelSegments Answered
- onurerdoganmd
- November 09, 2021 20:52
0 votes 15 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.