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No, you need to ignore them just as you would for all variant-calling applications. If they're duplicates then they're PCR or optical duplicates and potential sources of bias. To eliminate the bias remove them or mark them for downstream variant calling applications. About the only time this isn't done routinely is for RNA-Seq expression studies.
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Duplicated Reads for Somatic Mutation Detection
Hello, everyone,
There is one question about somatic mutation detection, is there anyone could help me?
Duplicated reads may be marked by Picard in bam-files, and most software don't care this tag. When we calculate CNVs, we shouldn't use duplicated reads, How about Somatic SNVs or InDels?Tags: None
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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