Somatic
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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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Make panel of normal with various conditions0 votes 1 comment
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Mutect2 somatic mutation filtering0 votes 4 comments
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GATK Mutect 2 can't call a true positive variant0 votes 10 comments
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Quality Drop in BAM Files After BaseRecalibrator0 votes 1 comment
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Filtering out germline calls with exact binomial test1 vote 2 comments
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Assembled haplotypes look very artificial0 votes 2 comments
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Somatic variants lost when --genotype-germline-sites true0 votes 3 comments
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Calculating variations between two tumor states0 votes 1 comment
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low af variant with contamination tag0 votes 3 comments
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Reproduce GATK Tutorial#11682 leading to different results0 votes 3 comments
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Confusing Mutect2 F1R2 (_f1r2.tar.gz) outputs0 votes 7 comments
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Slippage filter and multi-tool indel consensus calling0 votes 3 comments
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Mutect2 Stall on Chromosome 30 votes 5 comments
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Mutect2 Variant has very long ALT allele0 votes 8 comments
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Calling somatic CNV over multiple intervals and join them subsequently0 votes 4 comments
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GATK Picard SortSam/MarkDups Error with Snappy Loading0 votes 3 comments
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GATK ModelSegments result0 votes 3 comments
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Mutect2 Shared Variant PASS in one tumor sample, but not other samples0 votes 11 comments
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Funocator chromosome missmatch to somatic variant calling pipeline0 votes 4 comments
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FilterMuectCalls program request *vcf.stats file0 votes 3 comments