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
CNNScoreVariants ImportError: cannot import name 'Adam' Answered
- albert son
- August 17, 2022 21:10
1 vote 1 comment
Variant filtered from GVCF Answered
- LP
- June 14, 2022 14:15
1 vote 9 comments
Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app
- Jason Ni
- April 20, 2022 21:29
1 vote 5 comments
FilterVariantTranches Error: 'no variants with INFO score key "CNN_2D"' Answered
- Cher Wei Yuan
- December 13, 2021 03:38
- Edited
1 vote 7 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
BaseRecalibrator - no suitable codecs Answered
- Rhodri Smith
- April 01, 2020 09:59
1 vote 14 comments
MarkDuplicatesSpark consumes enormous amount of RAM Answered
- Yangyxt
- March 11, 2020 02:20
1 vote 25 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
Convert combineGVCF result to GenomicsDB [Repost] Answered
- Jing Yu
- February 13, 2020 12:45
- Edited
1 vote 14 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
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

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