Germline
Forum thread to discuss GATK Germline tools
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gCNV2 votes 1 comment
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GATK4.1.5 GenotypeGVCFs --annotation-group2 votes 1 comment
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How do I SelectVariants from GenomicsDB stored in GCS?1 vote 12 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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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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Missing PS field in the VCF file produced by GenotypeGVCFs1 vote 6 comments
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RNAseq short variant discovery pipline has the unused interval file0 votes 0 comments
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HaplotypeCaller rounded AF ?0 votes 2 comments
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HaplotypeCaller - incompatible contigs (one scaffold only)0 votes 4 comments
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humanG1Kv37 (b37) to hg38 liftover issues0 votes 4 comments
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DetermineGermlineContigPloidy error0 votes 1 comment
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Haplotypes of duplicated genes0 votes 1 comment
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Joint variant calling of WGS and RNAseq GVCF files0 votes 2 comments
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Funcotator table format0 votes 1 comment
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variantReCallibrator0 votes 1 comment
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The optimization step for ELBO update returned a NaN0 votes 3 comments
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GenomicsDBImport syntax error0 votes 1 comment