Somatic
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GATK Mutect2 "--germline-resource" and "--panel-of-normals" for reference hg190 votes 10 comments
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Using GATK ASE read counter with strelka0 votes 2 comments
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Difference in results between salmon and ASEReadCounter0 votes 2 comments
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Mismatch between mutect2 VCF and IGV BAM stats (causing strand bias issue)0 votes 3 comments
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normal-lod documentation is misleading0 votes 7 comments
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Mutect2 genotype for multiple Tumor samples0 votes 1 comment
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Getting the variant counts0 votes 4 comments
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Funcotator - Unexpected value: Ensembl_canonical0 votes 5 comments
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How number of somatic variants in the sample affects Mutect2 results?1 vote 0 comments
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mutect2 results0 votes 1 comment
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Long deletion split into two deletions nearby an SNV.0 votes 1 comment
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Value was put into PairInfoMap more than once0 votes 1 comment
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Mutect2 (normal BAM = FFPE-degraded, fragmented Low-DP)0 votes 3 comments
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FilterMutectCalls Problems0 votes 3 comments
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Number of mutations differs between WES kits0 votes 4 comments
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Mutect2 GVCF0 votes 1 comment
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GATK Mutect 2 can't call a true positive variant0 votes 10 comments
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Filtering out germline calls with exact binomial test1 vote 2 comments
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Mutect2 somatic mutation filtering0 votes 4 comments
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Make panel of normal with various conditions0 votes 1 comment
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Quality Drop in BAM Files After BaseRecalibrator0 votes 1 comment
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normal sample AF in Mutect2 paired mode1 vote 3 comments