Somatic
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strand bias and orientation bias5 votes 2 comments
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Custom made Panel of Normals required?2 votes 2 comments
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Generating ACS like output from new GATK CNV pipeline (WGS)2 votes 4 comments
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How number of somatic variants in the sample affects Mutect2 results?1 vote 0 comments
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Filtering out germline calls with exact binomial test1 vote 2 comments
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SOLVED: Get read counts of Mutect2 somatic variants1 vote 1 comment
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Mutect2 - No .stats file created with SLURM1 vote 2 comments
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normal sample AF in Mutect2 paired mode1 vote 3 comments
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Funcotator maf has different alt allele than vcf for some variants1 vote 1 comment
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MarkDuplicatesSpark error missing Read Group fields1 vote 1 comment
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CalculateContamination "there is no such column: contig"1 vote 8 comments
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gatk CollectAllelicCounts error1 vote 6 comments
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Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations1 vote 15 comments
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Permissions on gs://broad-references1 vote 4 comments
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Mutect2 - somatic variant calling with/without matched normal sample1 vote 14 comments
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MergeBamAlignment Error: ArrayIndexOutOfBoundsException1 vote 3 comments
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Problems combining gVCFs that have thousands of scaffolds1 vote 5 comments
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Call germline mutations from Mutect21 vote 3 comments
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normal-lod documentation is misleading0 votes 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