Germline
Forum thread to discuss GATK Germline tools
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Jointgenotyping Genomicsdbimport failed for no obvious reasons1 vote 1 comment
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CNNScoreVariants ImportError: cannot import name 'Adam' Answered1 vote 1 comment
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Variant filtered from GVCF Answered1 vote 9 comments
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Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app1 vote 5 comments
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FilterVariantTranches Error: 'no variants with INFO score key "CNN_2D"' Answered1 vote 7 comments
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How do I SelectVariants from GenomicsDB stored in GCS?1 vote 27 comments
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how can i set num of cores when use haplotypecaller1 vote 3 comments
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Why do I see no evidence of alt allele in GVCF?1 vote 2 comments
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issue with gatk4-exome-analysis-pipeline when running given sample data1 vote 6 comments
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Can I continue to run Haplotypecaller when it is broken?1 vote 2 comments
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BaseRecalibrator - no suitable codecs Answered1 vote 14 comments
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MarkDuplicatesSpark consumes enormous amount of RAM Answered1 vote 25 comments
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read starts with deletion. Cigar: 4D150M1 vote 4 comments
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hg38 alt aware mode1 vote 4 comments
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HaplotypeCaller error: Read is malformed: read starts with deletion1 vote 21 comments
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Calling variants on chromosome Y1 vote 5 comments
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unable to create contig_ploidy_model1 vote 3 comments
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Convert combineGVCF result to GenomicsDB [Repost] Answered1 vote 14 comments
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Difference between GATK3.3 and GATK4.01 vote 1 comment
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Missing PS field in the VCF file produced by GenotypeGVCFs1 vote 6 comments
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erro in VQSR (WGS)0 votes 1 comment
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variant calling: dict and indexing0 votes 1 comment
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Has too many alleles in the combined VCF record0 votes 1 comment
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FastaAlternateReferenceMaker creating chimera0 votes 1 comment
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GATK gCNV Calling pipeline error0 votes 0 comments
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Missing RawGtCount annoation from GenotypeGVCF output0 votes 5 comments
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Unable to trim uncertain bases without flow order information0 votes 0 comments