Germline

Forum thread to discuss GATK Germline tools

Variant filtered from GVCF
- LP
- June 14, 2022 14:15
1 vote 9 comments
Funcotator - all IGR classification Answered
- Noam Rudberg
- May 25, 2022 11:06
0 votes 10 comments
Ambiguity in Germline short variant best practices
- nicksmith
- May 24, 2022 14:56
0 votes 1 comment
Funcotator Misconfigured Error (All IGR Annotations) Answered
- Gus Fridell
- May 20, 2022 21:31
0 votes 6 comments
DetermineGermlineContigPloidy error: line 137 Answered
- Carlos García Peral
- May 14, 2022 01:04
0 votes 3 comments
python exited with 135 in germlinecnvcaller
- shun inoue
- April 24, 2022 07:14
- Edited
0 votes 5 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
Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app
- Jason Ni
- April 20, 2022 21:29
1 vote 5 comments
SelectVariants error: Multiple Criteria Answered
- Harini Prasanna
- April 19, 2022 17:07
0 votes 3 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
B37 joint variant calling workflow says "for hg38 only" Answered
- Oliver Ruebenacker
- April 11, 2022 17:02
0 votes 1 comment
workspace.haplotype_database_b37
- Oliver Ruebenacker
- April 06, 2022 19:23
0 votes 1 comment
Program Record ID already in use in unmapped BAM file. Answered
- Oliver Ruebenacker
- March 31, 2022 21:19
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
Haplotypecaller 4.5.2.0 --alleles unexpected output Answered
- Geert Vandeweyer
- March 13, 2022 08:49
0 votes 7 comments
GenomicsDBImport error from # fields in AS_UNIQ_ALT_READ_COUNT Answered
- Jeff Gaither
- March 12, 2022 21:55
0 votes 3 comments
DetermineGermlineContigPloidy error with exome germline data Answered
- shun inoue
- March 02, 2022 04:25
- Edited
0 votes 5 comments
hs37d5 genome in the GATK bundle Answered
- Rea Kalampaliki
- February 17, 2022 10:16
- Edited
0 votes 3 comments
gatk GenotypeGVCFs produced an error Answered
- Lijun
- February 09, 2022 15:17
0 votes 7 comments
Difference in contigs between hg19_v0_Homo_sapiens_assembly19.fasta and hg19_v0_1000G_omni2.5.b37.vcf.gz and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf files? Answered
- Rea Kalampaliki
- February 09, 2022 11:30
- Edited
0 votes 3 comments
Error while running CreateReadCountPanelOfNormals Answered
- Elizaveta Kolganova
- February 04, 2022 20:06
-1 votes 4 comments
GATK v4.2.4.0 VariantAnnotator running too slow Answered
- Anson Wong
- January 29, 2022 11:08
- Edited
0 votes 21 comments
HaplotypeCaller's -bamout created BAM-file not showing reads even with --force-active and --output-mode EMIT_ALL_ACTIVE_SITES Answered
- Vee Koo
- January 13, 2022 11:56
- Edited
0 votes 3 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
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
selectvariants error when consolidating GVCFs Answered
- jingchun liu
- December 14, 2021 03:08
- Edited
0 votes 3 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
Haplotypecaller yields none mutation records Answered
- zhexin liu
- December 07, 2021 15:19
0 votes 1 comment

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