Documentation Questions
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HaplotypeCaller using one sample split in two bam files0 votes 1 comment
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germline mutation calling using per-sample module0 votes 1 comment
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Single sample germline - VQSR+CNN or just CNN0 votes 5 comments
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Genomes in the cloud docker file0 votes 0 comments
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What's wrong with my GATK HaplotypeCaller step's codes?0 votes 1 comment
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How can I get Sample Summary0 votes 1 comment
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GATK4.2.3.0 HaplotypeCaller error0 votes 1 comment
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How does Genomicsdbimport for polyploids work?0 votes 2 comments
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Difference between the different annotation groups available in GATK2 votes 1 comment
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Mark duplicates in merged bam files sorted by coordinates0 votes 2 comments
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What does PCT_MIX from CreateVerifyIDIntensityContaminationMetricsFile mean?0 votes 2 comments
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GenomicsDBImport java error0 votes 1 comment
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ApplyBQSRSpark ApplyBQSR has different results0 votes 3 comments
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Potential updates to GATK HaplotypeCaller documentation0 votes 1 comment
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Converting Reference Genomes from b37 to hg190 votes 4 comments
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Germline CNV vs HaplotypeCaller/indels0 votes 1 comment
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ASEReadCounter count each read only once or not0 votes 1 comment
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error-handling-end-exit-codes-in-gatk0 votes 1 comment
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What do the two different minimum base quality filters do in Mutect2?0 votes 3 comments
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Funcotator misses many Cosmic fields - update possible?0 votes 1 comment
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The base of logarithm for VQSLOD0 votes 1 comment
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GATK-CollectVariantCallingMetrics - regarding more information0 votes 1 comment
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Map reads to a reference with alternate contigs like GRCH38 using GATK40 votes 3 comments
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gCNV2 votes 1 comment