Germline
Forum thread to discuss GATK Germline tools
Show no status
Sort by comments
-
memory troubles and modified imports for pipeline running on Google Cloud0 votes 34 comments
-
GATKgCNV Error: "Some contigs do not have ploidy priors"0 votes 32 comments
-
How do I SelectVariants from GenomicsDB stored in GCS?1 vote 29 comments
-
Call copy number variants with GermlineCNVCaller0 votes 25 comments
-
erro running "gatk seq-format-validation workflow"0 votes 21 comments
-
HaplotypeCaller error: Read is malformed: read starts with deletion1 vote 21 comments
-
DP/AD in SNP greater than coverage in bamout?0 votes 20 comments
-
Missing RawGtCount annoation from GenotypeGVCF output0 votes 19 comments
-
Why Haplotypecaller gives me empty vcf (only the header) for all of my samples?0 votes 18 comments
-
.GenomicsDBException: Duplicate sample name found:0 votes 17 comments
-
Strategy for buildling GenomicsDB0 votes 17 comments
-
Number of variants: discordance between HC and CNN0 votes 17 comments
-
combineGVCF errors and questions: inconsistent references & combineGVCF twice0 votes 16 comments
-
Big variance of PCT_BASES_20X between software versions0 votes 16 comments
-
CombineGVCF on chrX and chrY hg38 running for ever0 votes 15 comments
-
Bamout looks much worse than original BAM, false positive calls?0 votes 15 comments
-
GATK Funcotator and GATK VariantFiltration0 votes 15 comments
-
GenomicsDBImport failing on 'conflicting field description'0 votes 14 comments
-
Germline CNV WDL - SIGKILL0 votes 13 comments
-
Sortvcf generated empty file. GATK40 votes 13 comments
-
BQSR returns lower scores for male samples0 votes 13 comments
-
GATK4 validateSam Errors interpretation0 votes 12 comments
-
Haplotype caller missed variant0 votes 12 comments
-
haplotycaller --alleles : arrayIndexOutofBoundsException0 votes 11 comments
-
Wrong allosomal ploidies from DetermineGermlineContigPloidy.0 votes 11 comments
-
GATK4 VariantAnnotator doesn't support AlleleBalance0 votes 11 comments
-
MarkduplicateSpark error0 votes 11 comments
-
The optimization step for ELBO update returned a NaN0 votes 11 comments