Germline
Forum thread to discuss GATK Germline tools
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Howto call germline SNPs from reads with MAPQ=00 votes 0 comments
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GenotypeGVCFs : VariantQueryProcessorException0 votes 2 comments
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Varinat PASS given Genotype quality = 00 votes 2 comments
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JointGenotyping.ImportGvcfs terminates without an active exception0 votes 4 comments
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HaplotypeCaller interval list0 votes 0 comments
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Jointgenotyping Genomicsdbimport failed for no obvious reasons1 vote 1 comment
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Cohort_denoising.py parameter issue in GermlineCNVCaller Answered0 votes 15 comments
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CNNScoreVariants ImportError: cannot import name 'Adam' Answered1 vote 1 comment
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gCNV SVLEN question0 votes 4 comments
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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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CombineVariants Doesnt produce output0 votes 1 comment
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Variant filtered from GVCF Answered1 vote 9 comments
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Funcotator - all IGR classification Answered0 votes 10 comments
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Ambiguity in Germline short variant best practices0 votes 1 comment
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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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python exited with 135 in germlinecnvcaller0 votes 5 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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Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app1 vote 5 comments
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SelectVariants error: Multiple Criteria Answered0 votes 3 comments
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B37 joint variant calling workflow says "for hg38 only" Answered0 votes 1 comment
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workspace.haplotype_database_b370 votes 1 comment
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Program Record ID already in use in unmapped BAM file. Answered0 votes 1 comment
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Haplotypecaller 4.5.2.0 --alleles unexpected output Answered0 votes 7 comments
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GenomicsDBImport error from # fields in AS_UNIQ_ALT_READ_COUNT Answered0 votes 3 comments