NGS - sample purity assesment
Entering edit mode
11 months ago
Pinhole • 0

Hello community! I am preparing for my master thesis in bioinformatics and I wondering if there are any tools to get the information about sample purity like:

  • amount of normal cells
  • amount of tumor cells
  • ..sample contamination (microorganisms etc.) - I already know that haplocheck would be a good fit for one use-case

I wrote a pipeline to analyse rna-seq and perform wes variant calling. The goal would be a neoantigen detection but before I continue I want to check if the analysis make sens on my data.

Most of the tools I found so far - such as ABSOLUTE is not fully open-source and is limited to one type of data. Are there any open-source tools that can be used for finding out the sample purity including all the potential data I have: -rna-seq -wes

Or are there any guidelines similar to GATK Best Practices Workflows for sample purity? Any advice is gold for me :)

ngs • 234 views

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