Germline

Forum thread to discuss GATK Germline tools

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
Missing RawGtCount annoation from GenotypeGVCF output
- Uday Evani
- January 21, 2023 01:23
- Edited
0 votes 19 comments
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
The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*
- Oliver Ruebenacker
- April 14, 2022 23:37
0 votes 16 comments
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
variant calling: dict and indexing
- Nagarajan Raju
- February 05, 2023 14:23
0 votes 1 comment
GATK gCNV Calling pipeline error
- Heejun Jang
- January 27, 2023 08:56
0 votes 0 comments
PostprocessGermlineCNVCalls extremely slow after JointGermlineCNVSegmentation and produces many artifacts on sexual chromosomes
- Tintest
- December 06, 2022 14:51
- Edited
0 votes 1 comment
How to get a SNPs file for chicken genome to be used for base-quality score recaliberation step of GATK variant calling
- Mohamed Samir
- December 20, 2022 12:44
0 votes 0 comments
GenotypeGVCFs : VariantQueryProcessorException
- Henri-Jean Garchon
- November 29, 2022 10:55
0 votes 5 comments
HaplotypeCaller interval list
- Leo B
- October 18, 2022 10:35
0 votes 1 comment
PostprocessGermlineCNVCalls generate a segment file with missing GT field for the segment file
- NawarDalila
- November 09, 2022 13:07
0 votes 3 comments
Howto call germline SNPs from reads with MAPQ=0
- LH LV
- December 01, 2022 09:22
0 votes 0 comments
Varinat PASS given Genotype quality = 0
- Matteo Orlandi
- November 14, 2022 14:05
0 votes 2 comments
humanG1Kv37 (b37) to hg38 liftover issues
- Nienke Biesot
- February 23, 2021 12:17
0 votes 6 comments
JointGenotyping.ImportGvcfs terminates without an active exception
- Elizabeth Lee
- October 19, 2022 17:47
0 votes 4 comments
gCNV SVLEN question
- Adriana
- August 12, 2022 15:15
0 votes 4 comments
Jointgenotyping Genomicsdbimport failed for no obvious reasons
- Jason Ni
- October 13, 2022 15:16
- Edited
1 vote 1 comment
CombineVariants Doesnt produce output
- nroak
- July 14, 2022 20:09
0 votes 1 comment
VariantFiltration ReadPosRankSum & MQRankSum undefined
- priyanka_surana
- February 20, 2020 23:45
0 votes 5 comments
Ambiguity in Germline short variant best practices
- nicksmith
- May 24, 2022 14:56
0 votes 1 comment
python exited with 135 in germlinecnvcaller
- shun inoue
- April 24, 2022 07:14
- Edited
0 votes 5 comments

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