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