Germline
Forum thread to discuss GATK Germline tools
-
erro in VQSR (WGS)0 votes 1 comment
-
variant calling: dict and indexing0 votes 1 comment
-
Has too many alleles in the combined VCF record0 votes 1 comment
-
FastaAlternateReferenceMaker creating chimera0 votes 1 comment
-
GATK gCNV Calling pipeline error0 votes 0 comments
-
Missing RawGtCount annoation from GenotypeGVCF output0 votes 5 comments
-
Unable to trim uncertain bases without flow order information0 votes 0 comments
-
Howto call germline SNPs from reads with MAPQ=00 votes 0 comments
-
GenotypeGVCFs : VariantQueryProcessorException0 votes 5 comments
-
Varinat PASS given Genotype quality = 00 votes 2 comments
-
JointGenotyping.ImportGvcfs terminates without an active exception0 votes 4 comments
-
HaplotypeCaller interval list0 votes 1 comment
-
Jointgenotyping Genomicsdbimport failed for no obvious reasons1 vote 1 comment
-
Cohort_denoising.py parameter issue in GermlineCNVCaller Answered0 votes 15 comments
-
CNNScoreVariants ImportError: cannot import name 'Adam' Answered1 vote 1 comment
-
gCNV SVLEN question0 votes 4 comments
-
should I worry if the tmp folder not empty after completing GenotypeGVCFs Answered0 votes 1 comment
-
Inconsistency between intervals.vcf and Normalized Copy ratios txt file in GCNV workflow 4.2.6.1 Answered0 votes 12 comments
-
BaseRecalibrator tool recalibration table Answered0 votes 1 comment
-
CombineVariants Doesnt produce output0 votes 1 comment
-
Variant filtered from GVCF Answered1 vote 9 comments
-
Funcotator - all IGR classification Answered0 votes 10 comments
-
Ambiguity in Germline short variant best practices0 votes 1 comment
-
Funcotator Misconfigured Error (All IGR Annotations) Answered0 votes 6 comments
-
DetermineGermlineContigPloidy error: line 137 Answered0 votes 3 comments
-
python exited with 135 in germlinecnvcaller0 votes 5 comments
-
The same number of SNPS and INDELS identified for all samples after joint genotyping Answered0 votes 12 comments