Germline
Forum thread to discuss GATK Germline tools
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[Repost] ReadGroup missing when Applying BQSR0 votes 41 comments
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Hg38 RNAseq germline variant calling – BQSR steps0 votes 33 comments
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HaplotypeCaller error: Read is malformed: read starts with deletion1 vote 21 comments
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DP/AD in SNP greater than coverage in bamout?0 votes 20 comments
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erro running "gatk seq-format-validation workflow"0 votes 19 comments
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Strategy for buildling GenomicsDB0 votes 17 comments
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Number of variants: discordance between HC and CNN0 votes 17 comments
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"htsjdk.samtools.SAMFormatException: Invalid GZIP header" in VariantRecalibrator0 votes 16 comments
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Big variance of PCT_BASES_20X between software versions0 votes 16 comments
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Unable to model correct base ploidy with DetermineGermlineContigPloidy0 votes 15 comments
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GATK Funcotator and GATK VariantFiltration0 votes 15 comments
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GenomicsDBImport failing on 'conflicting field description'0 votes 14 comments
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Convert combineGVCF result to GenomicsDB [Repost] Answered1 vote 14 comments
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.GenomicsDBException: Duplicate sample name found:0 votes 13 comments
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Germline CNV WDL - SIGKILL0 votes 13 comments
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Sortvcf generated empty file. GATK40 votes 13 comments
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BQSR returns lower scores for male samples0 votes 13 comments
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GATK4 validateSam Errors interpretation0 votes 12 comments
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How do I SelectVariants from GenomicsDB stored in GCS?1 vote 12 comments
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Haplotype caller missed variant0 votes 12 comments
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GenotypeGVCF by intervals0 votes 11 comments
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Genome STRiP SV Preprocess0 votes 11 comments
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Bamout looks much worse than original BAM, false positive calls?0 votes 11 comments
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Genomestrip CNVdiscoverypipeline failed running paralleled0 votes 11 comments
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GATK 4.1.7.0 VariantAnnotator Processing Speed Drop0 votes 11 comments
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Error while running CreateReadCountPanelOfNormals0 votes 11 comments
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BAM file and VCF file showing different results0 votes 11 comments
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Missing variant in VCF from GenotypeGVCFs0 votes 11 comments
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QualByDepth documentation issue0 votes 10 comments
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Determining disk size for running JointGenotyping workflow on Terra0 votes 10 comments