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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Question: Is possible to run Octupus with RNA-seq data? #251

Open alejandrogzi opened 1 year ago

alejandrogzi commented 1 year ago

Hi guys,

I was looking pipelines to detect variant with cancer RNA-seq data (STAR-2pass bam files). After giving a look to opossum-platypus, gatk and DeepVariant pipelines I found Octopus.

Is it possible to use Octopus with RNA-seq data? The pre-processing steps are the same?

Thanks in advance, Alejandro

TBradley27 commented 1 year ago

I am just another user, but I would suspect it would be better to use a specialised tool for this, which is designed to work with RNA-Seq data. There are many features of RNA sequencing data which make DNA variant callers inappropriate for this particular use case

jelber2 commented 1 year ago

As another user, it seems as though maybe one could use tools you mentioned above and then give octopus a try on just the sites other tools found? I think you would have to disable duplicate removal depending on your RNA-seq library preparation method (I.e., are there UMIs added ? For better duplicate removal in your data? ).