Germline
Forum thread to discuss GATK Germline tools
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Realign BAM getting stalled at a particular position for days0 votes 1 comment
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How to work with large data set with: GenomicsDBImport0 votes 1 comment
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BQSR0 votes 3 comments
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Recommended parameters for GenomicsDBImport0 votes 1 comment
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Sampletracking workflow using picard0 votes 1 comment
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Genome STRiP CNV Discovery pipeline error0 votes 5 comments
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Read groups0 votes 4 comments
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GenotypeGVCFs0 votes 1 comment
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GenomicsDBImport error due to GZIP header0 votes 3 comments
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Data pre-processing for variant discovery - BaseRecalibrator, vcf input?0 votes 6 comments
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Error when running HaplotypeCallerSpark0 votes 5 comments
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Error running gatk4-genome-processing-pipeline workflow0 votes 9 comments
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Variant calling in gene H19 disabled due to zero mapping quality0 votes 5 comments
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haplotypecaller DP much lower than apparent coverage0 votes 9 comments
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"htsjdk.samtools.SAMFormatException: Invalid GZIP header" in VariantRecalibrator0 votes 16 comments
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UnifiedGenotyper in GATK40 votes 1 comment
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Does the CN with LQ need to be deleted?0 votes 2 comments
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HaplotypeCaller ReassignOriginalMQAfterIndelRealignment0 votes 1 comment
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other reference in BaseRecalibrator known-sites option0 votes 3 comments
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MarkDuplicatesSpark substantially slower than original0 votes 5 comments
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VQSR - indel MQ zero variance and0 votes 1 comment
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Unable to perform variant filtration on GenomeSTRiP genotyped sites vcf0 votes 5 comments
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The Future of CNN Tools0 votes 2 comments