Germline
Forum thread to discuss GATK Germline tools
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Run VariantAnnotator on subset of samples0 votes 0 comments
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Getting HaplotypeCaller SNP support in tumor0 votes 0 comments
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HaplotypeCaller and low-VAF variants0 votes 3 comments
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Hg38 RNAseq germline variant calling – BQSR steps0 votes 7 comments
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CRAM to BAM conversion0 votes 1 comment
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Criteria to filter samples for Germline analysis0 votes 1 comment
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Genotype 0/1 for variants with VAF=80%0 votes 1 comment
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RNAseq - germline variant calling0 votes 3 comments
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[Repost] ReadGroup missing when Applying BQSR0 votes 16 comments
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Error: GATK Terra HaplotypeCaller Workflow0 votes 1 comment
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GenotypeGVCFs -all-sites outputs only VCF head, no obvious error0 votes 1 comment
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GenomicsDB incremental error0 votes 1 comment
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[Repost] ReadGroup missing when Applying BQSR0 votes 3 comments
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Why the indel in vcf 4.1 version has not FORMAT/DP0 votes 1 comment
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Reference genome to use0 votes 1 comment
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GenotypeGVCFs output has N-1 sample data0 votes 1 comment
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Unclear why Picard is erroring / no output produced0 votes 4 comments
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RNAseq - germline variant calling0 votes 3 comments
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how can i set num of cores when use haplotypecaller1 vote 3 comments
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About HaplotypeCaller article0 votes 4 comments
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SplitNCigarReads generating truncated bam files0 votes 1 comment
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How to covert gVCF to VCF0 votes 1 comment
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Workflow hanging on Google Cloud Life Sciences0 votes 3 comments
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GenotypeGVCF by intervals0 votes 11 comments
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How do I link adjacent variants from a haplotypercaller output vcf?0 votes 3 comments
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SingleExome on Cromwell on GCP VM stuck at Baserecalibrator [RAM issues]0 votes 3 comments
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How do I call denovo variants from trio cohort?0 votes 1 comment