Non-Human

gatk-microbialmode.jar
- Jian Wang
- March 23, 2023 21:33
0 votes 0 comments
known-sites for Felis_catus_9.0 (GCA_000181335.4) Answered
- Vladimir Makarov
- March 15, 2023 20:16
0 votes 4 comments
How to remove strand bias from a virus-derived signal-end NGS dataset
- Fadi Alnaji
- March 02, 2023 08:26
0 votes 4 comments
HaplotypeCaller not calling variants in the beginning of an alignment (except when --alleles is specified)
- Bert Bogaerts
- February 03, 2023 16:09
0 votes 1 comment
Tribble never saw the required #CHROM header, but it is there for the program GenomicsDBImport
- Zubayr Ahmad
- January 23, 2023 17:08
0 votes 2 comments
GATK HaplotypeCaller for non-model organism: gVCF output
- Katie
- January 12, 2023 18:17
0 votes 0 comments
Somatic Variant Calling for a non-model species not finding any variants
- Isabella Livingston
- January 09, 2023 16:58
0 votes 0 comments
GenotypeGVCF error
- Akshaya Vasudevan
- December 01, 2022 17:39
- Edited
0 votes 0 comments
The expected variants were not detected for pig RNA-seq by GATK
- Wen-ye Yao
- October 24, 2022 14:12
- Edited
1 vote 8 comments
GatherVcfs to concatenate GVCFs
- sanjeevksh
- October 22, 2022 00:38
0 votes 3 comments
GenotypeGvcf tetraploids as diploids Answered
- julien leuenberger
- August 12, 2022 09:26
0 votes 4 comments
GATK for Rnor6 - Funcotator error Answered
- Ngoc Khoi Dang
- August 03, 2022 16:30
- Edited
0 votes 1 comment
java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1 Answered
- Zane Swaydan
- June 30, 2022 11:38
- Edited
0 votes 8 comments
All intervals were filtered in Filterintervals
- 侯旻
- May 31, 2022 08:24
0 votes 11 comments
FindBreakpointEvidenceSpark sudden shutdown Answered
- Domniki Manousi
- March 07, 2022 12:01
0 votes 4 comments
emit-ref-confidence error Answered
- Camila Martínez Avila
- February 08, 2022 00:44
0 votes 3 comments
gatk4-4.2.4.0-0 Fixmate Error Answered
- Abrish
- January 26, 2022 10:25
- Edited
0 votes 2 comments
GATK HaplotypeCaller disable filter -DF with the error in positional argument value Answered
- Frans Dany
- January 14, 2022 03:00
0 votes 1 comment
VariantEval does not work or something wrong with my ref genome and dbsnps? Answered
- Anh Mai
- January 04, 2022 10:45
0 votes 5 comments
ValidateSamFile Error Answered
- Abrish
- January 04, 2022 14:11
- Edited
0 votes 1 comment
Query regarding CombineGVCFs Answered
- Abrish
- December 20, 2021 17:54
0 votes 4 comments
Inconsistent variant call in some pool-seq samples Answered
- Lorena
- December 10, 2021 15:53
0 votes 3 comments
Selectvariants for SNPs selection produces .vcf file without homozygous-REF calls
- Amod Kumar
- December 02, 2021 11:03
0 votes 5 comments
GatherVcfs - File number limit?
- rokkineste
- November 22, 2021 12:14
- Edited
0 votes 3 comments
GATK GenotypeGVCFs stuck on starting traversal Answered
- Mary Happ
- November 11, 2021 19:38
- Edited
0 votes 7 comments
How do iquery VCF for specific variants by CHROM and POS
- Alon Ziv
- October 30, 2021 09:40
0 votes 3 comments
No downsampling with max-reads-per-alignment-start
- Liang Ye
- October 28, 2021 01:37
- Edited
0 votes 3 comments
ArtificialHaplotypeRG makes variant heterozygous Answered
- Wiebe Kooistra
- September 29, 2021 14:34
0 votes 5 comments
GenomicsDBimport and CombineGVCF does not show variants at ~500 Mbp onwards, although gvcf files from HapolypeCaller report variants
- Hanin
- September 27, 2021 07:22
- Edited
0 votes 7 comments
is it ok to apply BQSR and HaplotypeCaller to autosome noncoding region by -L by chromoosme?
- Shanshan
- September 09, 2021 02:44
0 votes 2 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.