General Discussion
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what is a Good Cigar?0 votes 2 comments
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BQSR workflow for non-model organism0 votes 1 comment
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HaplotypeCaller not working for sort bam files0 votes 2 comments
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CalculateContamination inputs for paired tumor-normal data0 votes 2 comments
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HaplotypeCaller calling whole chromosome as NON_REF0 votes 1 comment
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GATK CNV caller cohort mode long running0 votes 2 comments
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How to identify differential microsatellites in GATK ?0 votes 1 comment
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Variant Filtering problem after merging0 votes 1 comment
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GATK Handling of Paralogs0 votes 1 comment
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Mutect2 Variant Filters0 votes 2 comments
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No Pileup Tables Answered0 votes 16 comments
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GenomicsDBImport Answered0 votes 3 comments
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Joint calling a mixed cohort (WES and WGS )0 votes 1 comment
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Differences between GATK 3.5 and 4.2.50 votes 1 comment
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Mutect2 calling 0/1 genotypes at sites with no reference base calls0 votes 1 comment
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Differentiating variant site from Force call or de novo0 votes 2 comments
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picard CompareSAMs0 votes 1 comment
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problem with GATK ASEReadCounter0 votes 4 comments
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Mutect2 size of indels detected?0 votes 1 comment
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Recommended tool for obtaining thresholded covered genomic regions0 votes 2 comments
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Mutations in contiguous sites within a sample0 votes 4 comments
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DepthOfCoverage: does --gene-list honour restrictions set by --intervals? Answered0 votes 2 comments
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HAPLOTYPE_MAP in CrosscheckFingerprints (Picard)0 votes 2 comments
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FastqToSam gives me wrong output for read pairs Answered0 votes 4 comments
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CombineGVCFs-VCFHeader Answered0 votes 2 comments
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BaseRecalibrator--known-sites Answered0 votes 2 comments
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GATK Mutect2 PON mus musculus vcf file conversion Answered0 votes 2 comments