Germline

Forum thread to discuss GATK Germline tools

[Repost] ReadGroup missing when Applying BQSR Answered
- Robinn Teoh
- January 06, 2021 23:35
0 votes 44 comments
Hg38 RNAseq germline variant calling – BQSR steps Answered
- manolis
- January 17, 2021 11:43
- Edited
0 votes 43 comments
Funcotator Error, incompatible contigs Answered
- J LoPiccolo
- September 28, 2021 23:41
0 votes 35 comments
BaseRecalibrator - no suitable codecs Answered
- Rhodri Smith
- April 01, 2020 09:59
1 vote 30 comments
MarkDuplicatesSpark consumes enormous amount of RAM Answered
- Yangyxt
- March 11, 2020 02:20
1 vote 25 comments
DetermineGermlineContigPloidy with exome germline data Answered
- S. Kose
- August 13, 2021 15:17
- Edited
0 votes 24 comments
GATK v4.2.4.0 VariantAnnotator running too slow Answered
- Anson Wong
- January 29, 2022 11:08
- Edited
0 votes 21 comments
"Did not inflate expected amount" Error Answered
- Jacob Wang
- November 02, 2021 08:27
0 votes 18 comments
"htsjdk.samtools.SAMFormatException: Invalid GZIP header" in VariantRecalibrator Answered
- zhaol
- October 13, 2020 14:17
- Edited
0 votes 18 comments
Cohort_denoising.py parameter issue in GermlineCNVCaller Answered
- Sayal Guirales
- September 14, 2022 16:07
0 votes 15 comments
Errors in bam files Answered
- Priyadarshini Thirunavukkarasu
- September 23, 2021 13:48
0 votes 14 comments
Variant not called with HaplotypeCaller Answered
- flora ponelle
- May 31, 2021 09:01
0 votes 14 comments
Haplotypecaller : variant calling not seen in bamout alignments Answered
- fabienne JABOT-HANIN
- May 27, 2021 11:21
0 votes 14 comments
Bug in GATK4 variant calling followed by CalculateGenotypePosteriors Answered
- G E
- April 02, 2021 17:49
- Edited
0 votes 14 comments
Convert combineGVCF result to GenomicsDB [Repost] Answered
- Jing Yu
- February 13, 2020 12:45
- Edited
1 vote 14 comments
GATK concordance Answered
- Priyadarshini Thirunavukkarasu
- November 11, 2021 11:08
- Edited
1 vote 13 comments
Inconsistency between intervals.vcf and Normalized Copy ratios txt file in GCNV workflow 4.2.6.1 Answered
- SkyWarrior
- July 30, 2022 16:32
0 votes 12 comments
The same number of SNPS and INDELS identified for all samples after joint genotyping Answered
- Vincent Appiah
- April 21, 2022 22:34
- Edited
0 votes 12 comments
emit-ref-confidence error using single sample BAM Answered
- suzy_bunters
- March 04, 2021 17:54
0 votes 11 comments
GATK Liftover memory issues on cohort vcf Answered
- Jose Arcadio Buendia
- August 24, 2020 21:59
0 votes 11 comments
GermlineCNVCaller/denoising_config.json Answered
- Yokofakun
- June 18, 2020 06:58
0 votes 11 comments
genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file Answered
- Jennifer Irving-McGrath
- January 23, 2020 16:58
0 votes 11 comments
Funcotator - all IGR classification Answered
- Noam Rudberg
- May 25, 2022 11:06
0 votes 10 comments
New version of GATK leads to VariantRecalibrator error. Answered
- woodword
- November 12, 2020 08:57
- Edited
0 votes 10 comments
Unparsable vcf record with allele * Answered
- Madison Strain
- April 16, 2020 13:21
0 votes 10 comments
Variant filtered from GVCF Answered
- LP
- June 14, 2022 14:15
1 vote 9 comments
CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:" Answered
- Yokofakun
- March 17, 2020 09:13
0 votes 9 comments
Unable to trim uncertain bases without flow order information Answered
- Laura Sanz
- December 21, 2022 02:41
- Edited
0 votes 8 comments
Abnormal Results from GATK HaplotypeCaller --different variant Call from the fastq and its downsample fastq from the same fastqdata Answered
- Amy zhang
- January 12, 2022 08:29
- Edited
0 votes 8 comments
genomicDBimport ERROR: java.lang.NumberFormatException: For input string Answered
- @Anna
- April 13, 2021 16:30
0 votes 8 comments

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