Germline
Forum thread to discuss GATK Germline tools
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How do I call denovo variants from trio cohort?0 votes 1 comment
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Funcotator doesn't work with jointgenotyping mutisample vcfs0 votes 1 comment
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CombineGVCF with a mix of gatk3 and gatk4 gvcf files.0 votes 1 comment
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Multi-sample VCF for CNV calling0 votes 1 comment
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VQSR binned chromosome VCFs0 votes 3 comments
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Malformed VCF; less genotypes present than required by header0 votes 3 comments
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Combine and Genotype GVCF - running time0 votes 1 comment
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Mixing up GATK versions0 votes 1 comment
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Genome STRiP SV Preprocess0 votes 11 comments
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CNN - conda python error0 votes 2 comments
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Read Names of Public Fastq Files incompatible with Picard's MarkDuplicates0 votes 3 comments
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Don't know why I am getting error at GenotypeVCFs step0 votes 4 comments
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How can I get AF for each sample in GVC JointGenotyping mode?0 votes 3 comments
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Speeding up GenotypeGVCFs from genomicsdb0 votes 7 comments
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Counld I use bam files from HISAT2 to call snp/indels?0 votes 1 comment
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New version of GATK leads to VariantRecalibrator error.0 votes 4 comments
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Error running basic gatk-workflows (seq-format-validation).0 votes 9 comments
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What is contig ploidy priors table and how to make it?0 votes 1 comment
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Best practice to deal with spanning deletion for downstream analysis0 votes 2 comments
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What is cohort?0 votes 1 comment
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How do I obtain fastq files from a bam file?0 votes 4 comments
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Detect other jobs writing to GenomicDB with GenomicDBImport0 votes 1 comment
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Difference between GATK Germline CNV Pipeline vs Genome STRiP?0 votes 8 comments
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GenomicsDBImport0 votes 1 comment
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Accept PR for gatk-workflows / gatk4-rnaseq-germline-snps-indels0 votes 2 comments