Germline
Forum thread to discuss GATK Germline tools
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BaseRecalibrator - no suitable codecs Answered1 vote 30 comments
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genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file Answered0 votes 11 comments
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why I have a 1/1 genotype on chromosome X for males Answered0 votes 6 comments
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emit-ref-confidence error using single sample BAM Answered0 votes 11 comments
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Unable to trim uncertain bases without flow order information Answered0 votes 8 comments
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mtDNA calling problems Answered0 votes 3 comments
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GATK GenomicsDBimport Error with TileDB Answered1 vote 2 comments
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Can't generate ploidy-calls directory and ploidy-calls/SAMPLE_0 when use DetermineGermlineContigPloidy Answered0 votes 2 comments
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Before using GATK, do I need to use short-read error correction tools such as RACER or HiTEC? Answered0 votes 1 comment
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Why the genedb needs 'appropriate extension' in GenotypeGVCFs? Answered0 votes 3 comments
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GermlineCNVCaller in CASE mode using too many CPU for denoising Answered0 votes 4 comments
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Haplotypecaller too long ? Answered0 votes 6 comments
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DetermineGermlineContigPloidy with exome germline data Answered0 votes 24 comments
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Input configuration for GATK4-gCNV workflow on Terra Answered0 votes 5 comments
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Cohort_denoising.py parameter issue in GermlineCNVCaller Answered0 votes 15 comments
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CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:" Answered0 votes 9 comments
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CNNScoreVariants ImportError: cannot import name 'Adam' Answered1 vote 1 comment
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should I worry if the tmp folder not empty after completing GenotypeGVCFs Answered0 votes 1 comment
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Inconsistency between intervals.vcf and Normalized Copy ratios txt file in GCNV workflow 4.2.6.1 Answered0 votes 12 comments
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BaseRecalibrator tool recalibration table Answered0 votes 1 comment
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GATK concordance Answered1 vote 13 comments
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Funcotator - all IGR classification Answered0 votes 10 comments
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Variant filtered from GVCF Answered1 vote 9 comments
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Funcotator Misconfigured Error (All IGR Annotations) Answered0 votes 6 comments
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DetermineGermlineContigPloidy error: line 137 Answered0 votes 3 comments
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The same number of SNPS and INDELS identified for all samples after joint genotyping Answered0 votes 12 comments
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Values for InbreedingCoeff annotation not detected for ANY training variant Answered0 votes 6 comments
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B37 joint variant calling workflow says "for hg38 only" Answered0 votes 1 comment
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SelectVariants error: Multiple Criteria Answered0 votes 3 comments
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MarkDuplicatesSpark consumes enormous amount of RAM Answered1 vote 25 comments