Germline
Forum thread to discuss GATK Germline tools
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[Repost] ReadGroup missing when Applying BQSR Answered0 votes 44 comments
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Hg38 RNAseq germline variant calling – BQSR steps Answered0 votes 43 comments
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Funcotator Error, incompatible contigs Answered0 votes 35 comments
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memory troubles and modified imports for pipeline running on Google Cloud0 votes 34 comments
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GATKgCNV Error: "Some contigs do not have ploidy priors"0 votes 32 comments
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BaseRecalibrator - no suitable codecs Answered1 vote 30 comments
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How do I SelectVariants from GenomicsDB stored in GCS?1 vote 29 comments
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Call copy number variants with GermlineCNVCaller0 votes 25 comments
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MarkDuplicatesSpark consumes enormous amount of RAM Answered1 vote 25 comments
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DetermineGermlineContigPloidy with exome germline data Answered0 votes 24 comments
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GATK v4.2.4.0 VariantAnnotator running too slow Answered0 votes 21 comments
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erro running "gatk seq-format-validation workflow"0 votes 21 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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Missing RawGtCount annoation from GenotypeGVCF output0 votes 19 comments
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Why Haplotypecaller gives me empty vcf (only the header) for all of my samples?0 votes 18 comments
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"Did not inflate expected amount" Error Answered0 votes 18 comments
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"htsjdk.samtools.SAMFormatException: Invalid GZIP header" in VariantRecalibrator Answered0 votes 18 comments
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.GenomicsDBException: Duplicate sample name found:0 votes 17 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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combineGVCF errors and questions: inconsistent references & combineGVCF twice0 votes 16 comments
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Big variance of PCT_BASES_20X between software versions0 votes 16 comments
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Cohort_denoising.py parameter issue in GermlineCNVCaller Answered0 votes 15 comments
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CombineGVCF on chrX and chrY hg38 running for ever0 votes 15 comments
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Bamout looks much worse than original BAM, false positive calls?0 votes 15 comments
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GATK Funcotator and GATK VariantFiltration0 votes 15 comments
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Errors in bam files Answered0 votes 14 comments