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Steps For GATK-gCNV pipleline on Exome Data0 votes 12 comments
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ApplyBQSR0 votes 10 comments
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VCF file SNP ID missing0 votes 9 comments
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DP for each variant bulk is skewed towards 50 and multiples of 500 votes 7 comments
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CollectInsertSizeMetrics can't find R0 votes 6 comments
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GATK MarkDuplicates Missing output file1 vote 5 comments
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GATK configration0 votes 5 comments
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Markduplicates0 votes 5 comments
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Estimate genotype proportions from filtered variants0 votes 5 comments
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Running best practices workflow step-by-step in command line1 vote 5 comments
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How to provide custom exon-intron annotation source in Funcotator0 votes 4 comments
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GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases0 votes 4 comments
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Issue with Running MuTect in GATK Version Compatibility0 votes 3 comments
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cnv_germline_case_workflow.wdl0 votes 3 comments
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PICARD/Gradle build fail0 votes 3 comments
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Mutect2 wdl interval list and scatter count0 votes 3 comments
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get the basics for Haplotypecaller0 votes 2 comments
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Is It Allowed To Submit An Entire Code For Review?0 votes 2 comments
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Interval list and the “Mate not found” error in WES data0 votes 2 comments
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Is there a way to preserve numeric genotypes with VariantsToTable?0 votes 2 comments
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Scatter Gather principle by chromosome on Gatk1 vote 2 comments
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Where can I download Homo_sapiens_assembly38.haplotype_database.txt0 votes 2 comments
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Mutect2 somatic mutation calling for plant0 votes 2 comments
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Scatter / Gather for BaseRecalibrator on a single human WES dataset0 votes 2 comments
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GATK-SV HPC VM hardware requirements0 votes 1 comment
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Mitochondrial pipeline requirement0 votes 1 comment
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ExomeSingleSample wdl0 votes 1 comment
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STAR and GATK RNAseq based SNP detection0 votes 1 comment
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Best practice with read groups0 votes 1 comment