Germline
Forum thread to discuss GATK Germline tools
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Variant Calling at Interval Boundaries in GATK2 votes 3 comments
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Calling variants on chromosome Y2 votes 7 comments
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GATK ApplyBQSR failing1 vote 2 comments
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Trio de novo variants calling pipeline confuse1 vote 4 comments
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Issue with RNA-seq Variant Calling Pipeline using GATK1 vote 3 comments
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GenotypeGVCF not getting all samples1 vote 1 comment
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Best human reference genome chm13v2?1 vote 1 comment
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GATK GenomicsDBimport Error with TileDB Answered1 vote 2 comments
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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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GATK concordance Answered1 vote 13 comments
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How do I SelectVariants from GenomicsDB stored in GCS?1 vote 29 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 5 comments
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BaseRecalibrator - no suitable codecs Answered1 vote 30 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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unable to create contig_ploidy_model1 vote 3 comments