Germline

Forum thread to discuss GATK Germline tools

erro in VQSR (WGS)
- JUN ZHOU
- February 06, 2023 16:02
0 votes 1 comment
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
Missing RawGtCount annoation from GenotypeGVCF output
- Uday Evani
- January 21, 2023 01:23
- Edited
0 votes 5 comments
Unable to trim uncertain bases without flow order information
- Laura Sanz
- December 21, 2022 02:41
- Edited
0 votes 0 comments
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
PostprocessGermlineCNVCalls extremely slow after JointGermlineCNVSegmentation and produces many artifacts on sexual chromosomes
- Tintest
- December 06, 2022 14:51
- Edited
0 votes 1 comment
Howto call germline SNPs from reads with MAPQ=0
- LH LV
- December 01, 2022 09:22
0 votes 0 comments
GenotypeGVCFs : VariantQueryProcessorException
- Henri-Jean Garchon
- November 29, 2022 10:55
0 votes 5 comments
Varinat PASS given Genotype quality = 0
- Matteo Orlandi
- November 14, 2022 14:05
0 votes 2 comments
PostprocessGermlineCNVCalls generate a segment file with missing GT field for the segment file
- NawarDalila
- November 09, 2022 13:07
0 votes 3 comments
JointGenotyping.ImportGvcfs terminates without an active exception
- Elizabeth Lee
- October 19, 2022 17:47
0 votes 4 comments
HaplotypeCaller interval list
- Leo B
- October 18, 2022 10:35
0 votes 1 comment
Jointgenotyping Genomicsdbimport failed for no obvious reasons
- Jason Ni
- October 13, 2022 15:16
- Edited
1 vote 1 comment
gCNV SVLEN question
- Adriana
- August 12, 2022 15:15
0 votes 4 comments
CombineVariants Doesnt produce output
- nroak
- July 14, 2022 20:09
0 votes 1 comment
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
Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app
- Jason Ni
- April 20, 2022 21:29
1 vote 5 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 14 comments
workspace.haplotype_database_b37
- Oliver Ruebenacker
- April 06, 2022 19:23
0 votes 1 comment
CombineGVCFs - KEY END found in VariantContext field INFO but this key isn't defined in the VCFHeader
- Ryan Sun
- March 21, 2022 02:41
0 votes 3 comments
BaseRecalibrator java.lang.NullPointerException
- Vishak Madhwaraj
- December 20, 2021 05:15
0 votes 1 comment
GATK GenotypeGVCFs changes HET to REF_ALT
- FGV
- December 18, 2021 19:51
0 votes 0 comments
BQSR and VQSR resource sequences
- jingchun liu
- December 14, 2021 20:59
0 votes 1 comment
CNNScoreVariants has no output and print java.lang.NullPointerException
- Shay Kinreich
- December 07, 2021 10:55
0 votes 7 comments
GermlineCNVCaller prefix string too short
- Ahmed S. Chakroun
- December 05, 2021 14:02
- Edited
0 votes 9 comments
Different panels detect the same site, there are two different annotations, somatic and germline
- cjz
- December 02, 2021 09:31
0 votes 3 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.