Germline

Forum thread to discuss GATK Germline tools

Jointgenotyping Genomicsdbimport failed for no obvious reasons
- Jason Ni
- October 13, 2022 15:16
- Edited
1 vote 1 comment
Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app
- Jason Ni
- April 20, 2022 21:29
1 vote 5 comments
How do I SelectVariants from GenomicsDB stored in GCS?
- Lucas Taniguti
- January 31, 2021 13:04
1 vote 27 comments
Difference between WARP Exome Germline Single Sample and gatk4-exome-analysis-pipeline
- Ana Stankovic
- January 06, 2021 16:37
1 vote 4 comments
how can i set num of cores when use haplotypecaller
- xuekai yang
- December 17, 2020 06:55
- Edited
1 vote 3 comments
Import GVCFs using GenomicsDBImport one chromosome at a time and parallel the jobs encounter a Duplicate Sample Name Error
- Yangyxt
- August 28, 2020 17:12
1 vote 8 comments
Why do I see no evidence of alt allele in GVCF?
- akemde
- August 26, 2020 20:37
1 vote 2 comments
issue with gatk4-exome-analysis-pipeline when running given sample data
- umang kumar
- June 17, 2020 13:24
1 vote 6 comments
Can I continue to run Haplotypecaller when it is broken?
- Sin Lee
- May 27, 2020 07:26
1 vote 2 comments
read starts with deletion. Cigar: 4D150M
- iOOv
- March 08, 2020 07:57
1 vote 4 comments
hg38 alt aware mode
- hirokomatsui
- March 06, 2020 00:38
1 vote 4 comments
HaplotypeCaller error: Read is malformed: read starts with deletion
- Sue John
- March 05, 2020 10:41
1 vote 21 comments
Calling variants on chromosome Y
- Damian Fermin
- February 20, 2020 12:51
1 vote 5 comments
unable to create contig_ploidy_model
- Vishal Mishra
- February 20, 2020 06:23
1 vote 3 comments
Difference between GATK3.3 and GATK4.0
- Daisy
- January 13, 2020 07:46
1 vote 1 comment
REPOST - GenomeSTRiP error: partition.genotypes.map.dat file missing at Stage 12
- ikeoluwao_o
- January 07, 2020 22:12
1 vote 5 comments
Missing PS field in the VCF file produced by GenotypeGVCFs
- Derek Caetano-Anolles
- January 07, 2020 14:31
1 vote 6 comments
Wrong allosomal ploidies from DetermineGermlineContigPloidy.
- Weichi
- March 31, 2023 07:40
- Edited
0 votes 0 comments
HaplotypeCaller: missing INDELs
- Mihail Halachev
- March 30, 2023 10:15
0 votes 0 comments
GenomicsDBImport vs CombineGVCFs
- Robert Zeibich
- March 29, 2023 05:24
- Edited
0 votes 0 comments
GenomicsDBImport error - non-standard non-IUPAC base
- Tristan Dennis
- March 22, 2023 16:53
- Edited
0 votes 1 comment
Extracting gene segments that is in anti-sense/negative strand
- Nagarajan Raju
- March 15, 2023 15:03
0 votes 1 comment
GATK Haplotypecaller is calling Heterozygous variant, but bamout doesn't reflect the read frequencies in gvcf file
- kvn95ss
- March 11, 2023 04:26
0 votes 0 comments
HaplotypeCaller - output g.vcf is not phased?
- Daniel Kolbe
- February 28, 2023 12:04
- Edited
0 votes 1 comment
GATK HaplotypeCaller results in empty vcf
- Sameer Hassan
- February 17, 2023 16:45
- Edited
0 votes 1 comment
GermlineCNVCaller Assertion Error: Some samples do not have read depth metadata
- Xscrapert
- February 14, 2023 07:50
0 votes 0 comments
variant calling: dict and indexing
- Nagarajan Raju
- February 05, 2023 14:23
0 votes 1 comment
Has too many alleles in the combined VCF record
- rq m
- February 03, 2023 21:01
0 votes 1 comment
FastaAlternateReferenceMaker creating chimera
- Puechmaille
- February 01, 2023 15:00
0 votes 1 comment
GATK gCNV Calling pipeline error
- Heejun Jang
- January 27, 2023 08:56
0 votes 0 comments

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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.