Germline
Forum thread to discuss GATK Germline tools
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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
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GT corresponds to 0 reads0 votes 1 comment
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Allele-specific VQSR in 4.1.7.00 votes 3 comments
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output BAM form ApplyBQSR query using --interval option0 votes 3 comments
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ApplyBQSR (or any other tools) default CRAM configuration lossless or not?0 votes 3 comments
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GATK4 validateSam Errors interpretation0 votes 12 comments
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How do I SelectVariants from GenomicsDB stored in GCS?1 vote 12 comments
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dbSNP version for GATK best practices pipeline0 votes 1 comment
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Truth set download page for BQSR0 votes 1 comment
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How do I choose the "optimal" VQSR sensitivity threshold for indels?0 votes 6 comments
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GATK Haplotypecaller0 votes 2 comments
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ApplyVQSR tranche sensitivity filtering0 votes 6 comments
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How do I merge genome-wide SV from multiple individuals?0 votes 4 comments
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De novo assembly0 votes 4 comments